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

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
13:947678

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
10:e13843

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
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.*

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

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
11(13):5999

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
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.* 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
257:199-210

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:baw089

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
93:376–384

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
11(4):994–1003

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
7(1):127

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
14(6):378–387

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
161(3):278-286

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
49(6):974–980

2011

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

Analyzing regulatory networks in bacteria

Nature Education
3(9):24

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
9:176

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
9(10):R154

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
7:53

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
21(1):16–20

2005