Julio Augusto Freyre-Gonzalez

Julio Augusto Freyre-Gonzalez
Universidad Nacional Autónoma de México | UNAM · Centre for Genomic Sciences

B.Sc., M.Sc., Ph.D.

About

45
Publications
3,546
Reads
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396
Citations
Citations since 2017
20 Research Items
194 Citations
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2017201820192020202120222023010203040
Additional affiliations
September 2012 - present
Universidad Nacional Autónoma de México
Position
  • Investigador Asociado “C” T.C.
Position
  • I have participated actively
Position
  • since its conception
Education
February 2006
Universidad Nacional Autónoma de México
Field of study
  • 1st Winter School of Genomics
February 2003 - February 2009
Instituto de Biotecnología, UNAM
Field of study
  • Biochemical Sciences/Computational Genomics/Systems Biology
November 2001
Universidad Nacional Autónoma de México and Universidad Juárez Autónoma de Tabasco
Field of study
  • 3rd Autumn School on Mathematical Biology

Publications

Publications (45)
Article
Full-text available
The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data...
Article
Full-text available
MicroRNAs play important roles in cancer biology. Calcitriol, the hormonal form of vitamin D3, regulates microRNAs expression in tumor cells. In the present study we asked if calcitriol would modify some of the components of the microRNA processing machinery, namely, Drosha and Dicer, in calcitriol-responsive cervical cancer cells. We found that ca...
Article
Full-text available
Transcription factors (TFs) modulate gene expression as a consequence of internal or exogenous changes in cell signaling. TFs can bind to DNA either with their effector bound (holo conformation), or as free proteins (apo conformation). With the aim of contributing to the understanding of the evolutionary fitness and organizational principles behind...
Article
Escherichia coli and Bacillus subtilis are two of the best-studied prokaryotic model organisms. Previous analyses of their transcriptional regulatory networks have shown that they exhibit high plasticity during evolution and suggested that both converge to scale-free-like structures. Nevertheless, beyond this suggestion, no analyses have been carri...
Article
Full-text available
Previous studies have used different methods in an effort to extract the modular organization of transcriptional regulatory networks. However, these approaches are not natural, as they try to cluster strongly connected genes into a module or locate known pleiotropic transcription factors in lower hierarchical layers. Here, we unravel the transcript...
Article
Full-text available
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to ge...
Article
Full-text available
Orthologs separate after lineages split from each other and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis bas...
Article
Full-text available
Synthetic biology aims to apply engineering principles for the rational, systematical design and construction of biological systems displaying functions that do not exist in nature or even building a cell from scratch. Understanding how molecular entities interconnect, work, and evolve in an organism is pivotal to this aim. Here, we summarize and d...
Article
Full-text available
Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. Even though S. coelicolor has an outstanding variety of regulators among bacteria, little effort to globally study its transcription has been made. We manually curated 29 years of literature and databas...
Preprint
Full-text available
Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. However, little effort to globally study its transcription has been made even though S. coelicolor has an outstanding variety of regulators among bacteria. We manually curated 29 years of literature and...
Preprint
Full-text available
Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. However, little effort to globally study its transcription has been made even though S. coelicolor has an outstanding variety of regulators among bacteria. We manually curated 29 years of literature and...
Article
Full-text available
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructe...
Article
Full-text available
Identifying groups that share common features among datasets through clustering analysis is a typical problem in many fields of science, particularly in post-omics and systems biology research. In respect of this, quantifying how a measure can cluster or organize intrinsic groups is important since currently there is no statistical evaluation of ho...
Preprint
Full-text available
Identifying groups that share common features among datasets through clustering analysis is a typical problem in many fields of science, particularly in post-omics and systems biology research. In respect of this, quantifying how a measure can cluster or organize intrinsic groups is important since currently there is no statistical evaluation of ho...
Preprint
Full-text available
Identifying groups that share common features among datasets through clustering analysis is a typical problem in many fields of science, particularly in post-omics and systems biology research. In respect of this, quantifying how a measure can cluster or organize intrinsic groups is important since currently there is no statistical evaluation of ho...
Preprint
Full-text available
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory interactions, which study at the global scale has been challenged by the lack of data integration. Here, we update the manually-curated C. glutamicum transcriptional regulatory network, now including protein-protein...
Preprint
Full-text available
Background: Orthologs diverge after speciation events and paralogs after gene duplication. It is thus expected that orthologs would tend to keep their functions, while paralogs could be a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synon...
Preprint
Full-text available
Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to heterogeneity across databases. Such heterogeneity mainly encompasses different names for a gene and different network...
Article
Full-text available
Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to heterogeneity across databases. Such heterogeneity mainly encompasses different names for a gene and different network...
Article
Full-text available
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed the distribution of GRN structural properties across a large set of distinct prokaryotic organisms and found...
Preprint
Full-text available
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network is currently complete. In this study, we analyzed the distribution of GRN structural properties across a large set of distinct prokaryotic organisms and found a s...
Preprint
Full-text available
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network is currently complete. In this study, we analyzed the distribution of GRN structural properties across a large set of distinct prokaryotic organisms and found a s...
Article
Corynebacterium glutamicum is a Gram-positive, anaerobic, rod-shaped soil bacterium able to grow on a diversity of carbon sources like sugars and organic acids. It is a biotechnological relevant organism because of its highly efficient ability to biosynthesize amino acids, such as L-glutamic acid and L-lysine. Here, we reconstructed the most comple...
Article
Full-text available
The regulation of gene expression at the transcriptional level is a fundamental process in prokaryotes. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possibl...
Article
Full-text available
In bacteria, transcriptional regulation is a key step in cellular gene expression. All bacteria contain a core RNA polymerase that is catalytically competent but requires an additional σ factor for specific promoter recognition and correct transcriptional initiation. The RNAP core is not able to selectively bind to a given σ factor. In contrast, di...
Data
Full-text available
Supplementary material is available on the publisher’s web site along with the published article.
Article
Full-text available
Pentachlorophenol is the most toxic and recalcitrant chlorophenol because both aspects are directly proportional to the halogenation degree. Biological and abiotic pentachlorophenol degradation generates p-chloranil, which in neutral to lightly alkaline environmental conditions is hydrolyzed to chloranilic acid that present a violet-reddish colorat...
Article
Full-text available
Bacteria express genes in response to environmental signals. Therefore, when scientists study gene expression in vitro, they must avoid the presence of any undesired signal in the medium. To avoid these undesired signals, scientists prepare growth media according well-defined formulas and grown bacteria under strictly controlled conditions. In natu...
Article
Full-text available
Glucose is the preferred carbon and energy source for Bacillus subtilis and Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzymatic activities, in response to the presence of this sugar. We present a comparison of the cellular response to glucose in these two model organisms, using an approach combining g...
Data
Supplementary Table 1SM. "VazquezHernandezSupplementary-Material_1" and contains tables from 1 to 3, describe in the manuscript as Table 1SM.
Data
Supplementary Tables 2-3SM. "VazquezHernandezSupplementary-Material_2" and contains Tables 2 to 3, described in the manuscript as Table 2aSM, Table 2bSM, and Table 3SM.
Data
Full-text available
Modules identified in this study and their manual and computational annotations.
Data
Full data set for the E. coli transcriptional regulatory network reconstructed for our analyses.
Data
Full-text available
Topological properties of the transcriptional regulatory network of E. coli.
Data
Full-text available
Intermodular genes found in this study, their biological descriptions and roles as integrative elements.
Article
Full-text available
Glucose is the preferred carbon and energy source for Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzyme activities in response to the presence of this sugar. To determine the extent of the cellular response to glucose, we applied an approach combining global transcriptome and regulatory network analyse...
Article
Full-text available
The transcriptional network of Escherichia coli is currently the best-understood regulatory network of a single cell. Motivated by statistical evidence, suggesting a hierarchical modular architecture in this network, we identified eight modules with well-defined physiological functions. These modules were identified by a clustering approach, using...
Conference Paper
Full-text available
El objetivo de esta investigación es el de evaluar técnicas bayesianas de clasificación aplicadas a la clonación conductista de operadores humanos. Para esto, se desarrolló y estudió un modelo probabilístico bayesiano, con discretización uniforme, para la clonación de habilidades de control de humano a máquina, basándose en el modelo de clonación c...

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Projects

Project (1)
Project
Objective: To discover the global properties governing TRN organization and finding thee evolutionary constraints that guides them.