Abasy Atlas


Natural decomposition approach


Our people


About us


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 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.

Featured Publications

  • 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

  • 2019

  • 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

  • Journal of Biotechnology

  • 2017

  • 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 (Oxford)

  • 2016

  • 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

  • 2012

  • Freyre-Gonzalez, J.A.* and Trevino-Quintanilla, L.G.

  • Analyzing regulatory networks in bacteria

  • Nature Education

  • 2010

  • Freyre-González, J.A.*, Alonso-Pavón, J.A., Treviño-Quintanilla, L.G., and Collado-Vides, J.

  • Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach

  • Genome Biology

  • 2008