Abasy Atlas

MORE

Natural decomposition approach

MORE

Our people

MORE

Laboratory of Systems and Synthetic Biology @ CCG, UNAM

MORE

About us

Aim

More
Freyre Lab

Our lab aims to develop novel techniques and methods to study and unveil the system-level principles governing the organization, function, and evolution of the large-scale biological circuitry. Studies in our lab range from the reconstruction and analysis of complex biological networks to comparative analyses of subsystems across different organisms, and from methods to naturally identify functional modules and other system-level components in gene circuitry to the large-scale massive prediction of molecular interactions from high-throughput data.

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 this, we integrate high-throughput data and different databases combining knowledge from molecular biology, complex systems theory, graph theory, computer science, statistics, mathematics, artificial intelligence, and machine learning.

Regarding teaching, since 2003 our group is responsible for the curricula and teaching of courses in computer science (“Programming Principles” and “Scientific Computing”). Additionally, we teach courses in systems biology and a workshop on this area having a teaching/research approach in the frontier of modern biological sciences. All these courses are taught for the Undergraduate Program in Genomic Sciences campus Morelos. Since the recent founding of the Undergraduate Program in Genomic Sciences ENES Juriquilla in 2018, we have been invited to participate in teaching the successful courses “Programming Principles” and “Scientific Computing”. We also teach graduate-level courses on the same areas for the Graduate Program in Biomedical Sciences and the Graduate Program in Biochemistry, both at the Universidad Nacional Autónoma de México.

Featured Publications

ALL

  • Escobedo-Muñoz, A.S., Carmona-Campos, D., Trapaga, A.G.G., Freyre-González, J.A.

  • How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO

  • Briefings in Bioinformatics
    26(5):bbaf560

  • 2025

  • Escorcia-Rodríguez, J.M., Gaytan-Nuñez, E., Hernandez-Benitez, E.M., Zorro-Aranda, A., Tello-Palencia, M.A., Freyre-González, J.A.

  • Improving gene regulatory network inference and assessment: The importance of using network structure

  • Frontiers in Genetics
    14:1143382

  • 2023

  • Freyre-Gonzalez, J.A.*, Escorcia-Rodríguez, J.M., Gutiérrez-Mondragón, L.F., Martí-Vértiz, J. Torres-Franco C.N., Zorro-Aranda, A.

  • System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks

  • Frontiers in Bioengineering and Biotechnology
    10:888732

  • 2022

  • 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

  • Escorcia-Rodríguez, J.M., Tauch, A., and 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

  • Campos, A.I. and 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

  • Freyre-González, J.A.*, Treviño-Quintanilla, L.G., Valtierra-Gutiérrez, I., Gutierrez-Ríos, R.M., and 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

  • Journal of Biotechnology
    161(3):278-286

  • 2012