Julio Augusto Freyre González

Systems Biology 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 and the Graduate Program in Biochemical Sciences, among others.

Links

http://freyrelab.org
Google Scholar
http://orcid.org/0000-0001-7061-7637
https://www.ncbi.nlm.nih.gov/pubmed/?term=Freyre-Gonz%C3%A1lez+JA%5BAuthor%5D
https://arxiv.org/a/freyregonzalez_j_1.html
ResearchGate
https://unam.academia.edu/jfreyre
https://publons.com/author/633264/julio-augusto-freyre-gonzalez
https://www.linkedin.com/in/jfreyreg
Thomson Reuters ResearcherID
OrcID
Scopus

Selected publications

Freyre-Gonzalez, J.A.*, Escorcia-Rodríguez, J.M., Gutiérrez-Mondragón, L.F., Martí-Vértiz, J. Torres-Franco C.N. y Zorro-Aranda, A. System principles governing the organization, architecture, dynamics, and evolution of gene regulatory networks. Frontiers in Bioengineering and Biotechnology 10 (2022) Artículo sometido por invitación a la edición especial sobre “Insights in Synthetic Biology 2021: Novel Developments, Current Challenges, and Future Perspectives” doi: 10.3389/fbioe.2022.888732.

Zorro-Aranda, A., Escorcia-Rodríguez, J.M., González-Kise, J.K., Freyre-González, J.A.* Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor. Scientific reports 12(1):2840 (2022) doi: 10.1038/s41598-022-06658-x.

Escorcia-Rodríguez, J.M., Tauch, A., y Freyre-González, J.A.* 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):1395 (2021) Artículo sometido por invitación a la edición especial sobre “Genetics and Physiology of Corynebacteria”. doi: 10.3390/microorganisms9071395.

Escorcia-Rodríguez, J.M., Tauch, A., y Freyre-González, J.A.* 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 (2020) doi: 10.1016/j.csbj.2020.05.015.

Campos-González, A.I. y Freyre-González, J.A.* Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. Scientific Reports 9(1):3618 (2019) doi: 10.1038/s41598-019-39866-z.

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.

Telephone: (777) 3291777 Ext. 38483
Email: jfreyre@ccg.unam.mx

Publications

YearPublicationPMID
2022Freyre-Gonzalez, Julio A., Escorcia-Rodriguez, Juan M., Gutierrez-Mondragon, Luis F., Marti-Vertiz, Jeronimo, Torres-Franco, Camila N., Zorro-Aranda, Andrea. (2022). "System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks.". Frontiers in bioengineering and biotechnology. 10():-. [doi:10.3389/fbioe.2022.888732]35646858
2022Zorro-Aranda, A., Escorcia-Rodríguez, J.M., González-Kise, J.K., Freyre-González, J.A.. (2022). "Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor.". SCIENTIFIC REPORTS. 12(1):2840-2840. [doi:10.1038/s41598-022-06658-x]35181703
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-BASEL. 11(13):-. [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
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
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
2016Ibarra-Arellano, M.A., Campos-González, A.I., Treviño-Quintanilla, L.G., Tauch, A., Freyre-González, J.A.. (2016). "Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2016():-. [doi:10.1093/database/baw089]27242034
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, J., Manjarrez-Casas, A.M., Merino. E., Martínez-Nuñez, M., Pérez, E., Gutiérrez, R.. (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, J., Treviño-Quintanilla, L.G., Valtierra, I., Gutiérrez, R., Alonso, J.. (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, J., 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, J., Alonso, J., Treviño, L., Collado, P.. (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, J., Resendis, O., Collado, P., 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, O., Freyre, J., Menchaca, R., Gutiérrez, R., Martínez, A., Ávila, C., Collado, P.. (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