• 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

  • 2023

  • Taboada-Castro, H., Gil, J., Gómez-Caudillo, L., Escorcia-Rodríguez, J.M., Freyre-González, J.A., Encarnación-Guevara, S.

  • Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network

  • Frontiers in Microbiology

  • 2022

  • Escorcia-Rodríguez, J.M., Esposito, M., Freyre-González, J.A., Moreno-Hagelsieb, G.

  • Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty

  • PeerJ

  • 2022

  • 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

  • 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

  • 2022

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

  • 2021

  • Camacho-Hernández, D.A., Nieto-Caballero, V.E., León-Burguete, J.E., and Freyre-González J.A.*

  • Partition Quantitative Assessment (PQA): A Quantitative Methodology to Assess the Embedded Noise in Clustered Omics and Systems Biology Data

  • Applied Sciences

  • 2021

  • 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

  • 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

  • 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

  • González-Duarte, R.J., Cázares-Ordoñez, V., Romero-Córdoba, S., Díaz, L., Ortíz, V., Freyre-González, J.A., Hidalgo-Miranda, A., Larrea, F., Avila, E.

  • Calcitriol increases Dicer expression and modifies the microRNAs signature in SiHa cervical cancer cells

  • Biochemistry and Cell Biology

  • 2015

  • Alvarez-Vasquez, F.J., Freyre-González, J.A., Balderas-Martínez, Y.I., Delgado-Carrillo, M.I., Collado-Vides, J.

  • Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli

  • Molecular Biosystems

  • 2015

  • Freyre-González, J.A., Manjarrez-Casas, A.M., Merino, E., Martinez-Nuñez, M., Perez-Rueda, E., and Gutiérrez-Ríos, R.M.

  • Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis

  • BMC Systems Biology

  • 2013

  • Treviño-Quintanilla, L.G., Freyre-González, J.A.§, and Martínez-Flores, I

  • Anti-Sigma Factors in E. coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability

  • Current Genomics

  • 2013

  • 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

  • Treviño-Quintanilla, L.G., Freyre-González, J.A., Guillén-Garcés, R.A., and Olvera-Carranza, C.

  • Molecular characterization of chloranilic acid degradation in Pseudomonas putida TQ07

  • Journal of Microbiology

  • 2011

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

  • Analyzing regulatory networks in bacteria

  • Nature Education

  • 2010

  • Vázquez, C.D., Freyre-González, J.A., Gosset, G., Loza, J.A., and Gutierrez-Ríos, R.M.

  • Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli

  • BMC Microbiology

  • 2009

  • 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

  • Gutierrez-Ríos, R.M., Freyre-González, J.A., Resendis, O., Collado-Vides, J., Saier, M., and Gosset, G.

  • Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli

  • BMC Microbiology

  • 2007

  • Resendis-Antonio, O., Freyre-González, J.A., Menchaca-Méndez, R., Gutiérrez-Ríos, R.M., Martínez-Antonio, A., Ávila-Sánchez, C., and Collado-Vides, J.

  • Modular analysis of the transcriptional regulatory network of E. coli

  • Trends in Genetics

  • 2005