Julio Augusto Freyre González

Systems Biology and Synthetic Biology Laboratory Researcher

Associate Professor

Academic history

Julio A. Freyre-González studied a B.Sc. in Computer Systems Engineering in the Veracruz Institute of Technology (ITVer) and a M.Sc. in Computer Science (Machine Learning) from the Monterrey Institute of Technology and Higher Education (ITESM). He was awarded a Ph.D. in Biochemistry (Computational Genomics) from the National Autonomous University of México (UNAM) in 2009.
During his master’s studies he developed a Bayesian methodology for behavioral cloning, which is a method to construct automatic control systems for complex tasks by capturing and reproducing human subcognitive skills in a computer program. After being impressed by problems on genomics and systems biology, he decided to go deeper in the field by studying a Ph.D. in Biochemistry. Then he turned his attention to the application of graph theory to study the topological properties and the modular and hierarchical organization of the transcriptional regulatory network of Escherichia coli. His work was a fundamental contribution to the first modular analysis of a bacterial regulatory network. During his doctoral research, he developed the foundations of the natural decomposition approach, a biological-mathematical framework that exploits the structural properties of regulatory networks to provide objective criteria enabling their decomposition and the identification of their system-level components.
Currently, his lab aims to develop novel techniques and methods to contribute to unveil the system-level principles governing the organization and evolution of large-scale biological circuitry. The long-term aim is to unveil evolutionary and system principles governing complex biological networks and to use this knowledge to develop novel strategies in synthetic biology. To accomplish these objectives, he integrate high-throughput data and different databases combining knowledge from molecular biology, graph theory, computer science, statistics, mathematics and artificial intelligence.
Julio Freyre has been awarded various prizes since he was an undergraduate, some of them are the 1st Young Software National Prize by the Arturo Rosenblueth Foundation in 1992, the 13th Young Talent in Life Sciences Prize (XIII Prêmio Jovem Talento em Ciências da Vida) by the Brazilian Society for Biochemistry and Molecular Biology (SBBq) and GE Healthcare Life Sciences in 2009, and the Morelos State Research Merit Award by the Government of Morelos in 2010.
He is also responsible for the curricula and teaching of courses in computer science (“Programming Principles” and “Scientific Computing”). This also include courses in systems biology, and a workshop on this area having a teaching/research approach in the frontier of biological sciences. These courses are taught in the Undergraduate Program in Genomic Sciences. We also teach graduate level courses on the same areas for the Graduate Program in Biomedical Sciences.


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Selected publications

Freyre-González, J.A.* and Tauch, A. Functional architecture and global properties of the Corynebacterium glutamicum regulatory network: novel insights from a dataset with a high genomic coverage. J. Biotechnol. 257C:199-210 (2017) doi: 10.1016/j.jbiotec.2016.10.025

Ibarra-Arellano, M.A., Campos-González, A.I., Treviño-Quintanilla, L.G., Tauch, A., Freyre-González, J.A.* Abasy Atlas: A comprehensive inventory of systems, global network properties, and systems-level elements across bacteria. Database 2016:baw089 (2016) doi: 10.1093/database/baw089

Freyre-González, J.A.*, Treviño-Quintanilla, L.G., Valtierra-Gutiérrez, I., Gutierrez-Ríos, R.M., y Alonso-Pavón, J.A. Prokaryotic regulatory systems biology: Common principles governing the functional architectures of Bacillus Subtilis and Escherichia coli unveiled by the natural decomposition approach. J. Biotechnol. 161(3):278-286 (2012) doi: 10.1016/j.jbiotec.2012.03.028

Freyre-Gonzalez, J.A.* y Trevino-Quintanilla, L.G. Analyzing regulatory networks in bacteria. Nature Education 3(9):24 (2010) http://www.nature.com/scitable/topicpage/analyzing-regulatory-networks-in-bacteria-14426192

Freyre-González, J.A.*, Alonso-Pavón, J.A., Treviño-Quintanilla, L.G., y Collado-Vides, J. Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. Genome Biol. 9(10):R154 (2008) doi: 10.1186/gb-2008-9-10-r154

Telephone: (777) 3133881
Email: jfreyre@ccg.unam.mx


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):5999-. [doi:10.3390/app11135999]
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
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
2017Freyre-González, J.A., Tauch, A.. (2017). "Functional architecture and global properties of the Corynebacterium glutamicum regulatory network: Novel insights from a dataset with a high genomic coverage". JOURNAL OF BIOTECHNOLOGY. 257():199-210. [doi:10.1016/j.jbiotec.2016.10.025]27829123
2015González-Duarte, R.J., Cázares-Ordoñez, V., Romero-Córdoba, S., Díaz, L., Ortíz, V., Freyre-González, J.A., Hidalgo-Miranda, A., Larrea, F., Avila, E.. (2015). "Calcitriol increases Dicer expression and modifies the microRNAs signature in SiHa cervical cancer cells". BIOCHEMISTRY AND CELL BIOLOGY. 93(4):376-384. [doi:10.1139/bcb-2015-0010]26111345
2015Alvarez-Vasquez, Fernando J., Freyre-Gonzalez, Julio A., Balderas-Martinez, Yalbi I., Delgado-Carrillo, Monica I., Collado-Vides, Julio. (2015). "Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli". Molecular Biosystems. 11(4):994-1003. [doi:10.1039/c4mb00561a]25683745
2013Freyre González, Julio Augusto, Manjarrez-Casas, A.M., Merino. E., Martínez-Nuñez, M., Pérez Rueda, Ernesto, Gutiérrez Ríos, Rosa María. (2013). "Lessons from the modular organization of the transcriptional regulatory network of Bacillus Subtilis". Bmc Systems Biology. 7():127-127. [doi:10.1186/1752-0509-7-127]24237659
2013Gerardo Trevino-Quintanilla, Luis, Augusto Freyre-Gonzalez, Julio, Martinez-Flores, Irma. (2013). "Anti-Sigma Factors in E-coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability". Current Genomics. 14(6):378-387. [doi:10.2174/1389202911314060007]24396271
2012Freyre González, Julio Augusto, Treviño-Quintanilla, L.G., Valtierra Gutiérrez, Ilse Ariadna, Gutiérrez Ríos, Rosa María, Alonso Pavón, José Antonio. (2012). "Prokaryotic regulatory systems biology: Common principles governing the functional architectures of Bacillus Subtilis and Escherichia coli unveiled by the natural decomposition approach". JOURNAL OF BIOTECHNOLOGY. 161(3):278-286. [doi:10.1016/j.jbiotec.2012.03.028]22728391
2011Trevino-Quintanilla, L.G., Freyre González, Julio Augusto, Guillén-Garces, R.A., Olvera, C.. (2011). "Molecular characterization of chloranilic acid degradation in pseudomonas putida TQ07". Journal Of Microbiology. 49(6):974-980. [doi:10.1007/s12275-011-1507-1]22203561
2008Freyre González, Julio Augusto, Alonso Pavón, José Antonio, Treviño Quintanilla, Luis Gerardo, Collado Vides, Pedro Julio. (2008). "Functional architecture of Escherichia coli: New insights provided by a natural decomposition approach". Genome Biology. 9(10):154-. [doi:10.1186/gb-2008-9-10-r154]18954463
2007Gutierrez-Rios, R.M., Freyre González, Julio Augusto, Resendis Antonio, Osbaldo, Collado Vides, Pedro Julio, Saier, M., Gosset, G.. (2007). "Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli". Bmc Microbiology. 7():53-53. [doi:10.1186/1471-2180-7-53]17559662
2005Resendis Antonio, Osbaldo, Freyre González, Julio Augusto, Menchaca Mendez, Ricardo, Gutiérrez Ríos, Rosa María, Martínez Antonio, Agustino, Ávila Sánchez, Cristhian, Collado Vides, Pedro Julio. (2005). "Modular analysis of the transcriptional regulatory network of E. coli". TRENDS IN GENETICS. 21(1):16-20. [doi:10.1016/j.tig.2004.11.010]15680508