Ernesto Perez Rueda
Ex-colaborador y/o ex-alumno
Total de publicaciones: 59
- Tipo
- Fecha
Artículo
1 - Avila-Mendoza, J., Perez-Rueda, E., Urban-Sosa, V., Carranza, M., Martinez-Moreno, C.G., Luna, M., Aramburo, C. (2018). Characterization and distribution of GHRH, PACAP, TRH, SST and IGF1 mRNAs in the green iguana.
General and Comparative Endocrinology,
255,
90-101.
Artículo
2 - Flores-Bautista, E., Ludena-Cronick, C., Rodriguez-Fersaca, A., Martinez-Nunez, M.A., Perez-Rueda, E. (2018). Functional prediction of hypothetical transcription factors of Escherichia coli K-12 based on expression data.
Computational and Structural Biotechnology Journal,
16,
157-166.
Artículo
3 - Martinez-Romero, E., Rodriguez-Medina, N., Beltran-Rojel, M., Silva-Sanchez, J., Barrios-Camacho, H., Perez-Rueda, E., Garza-Ramos, U. (2018). Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans.
Salud Publica de Mexico,
60 (1),
56-62.
Artículo
4 - Perez-Rueda, E., Hernandez-Guerrero, R., Martinez-Nunez, M.A., Armenta-Medina, D., Sanchez, I., Ibarra, J.A. (2018). Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.
PLoS ONE,
13 (4),
e0195332.
Artículo
5 - Brambila-Tapia, A.J.L., Perez-Rueda, E., Barrios, H., Davalos-Rodriguez, N.O., Davalos-Rodriguez, I.P., Cardona-Munoz, E.G., Salazar-Paramo, M. (2017). Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach.
Current Microbiology,
74 (8),
915-920.
Artículo
6 - Casella, L.G., Weiss, A., Perez-Rueda, E., Ibarra, J.A., Shaw, L.N. (2017). Towards the complete proteinaceous regulome of Acinetobacter baumannii.
Microbial Genomics,
3 (3),
mgen000107.
Artículo
7 - Martinez-Nunez, M.A., Rodriguez-Escamilla, Z., Rodriguez-Vazquez, K., Perez-Rueda, E. (2017). Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms.
Life (Basel),
7 (3).
Artículo
8 - Rivera-Gomez, N., Martinez-Nunez, M.A., Pastor, N., Rodriguez-Vazquez, K., Perez-Rueda, E. (2017). Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea.
Microbiology,
163 (8),
1167-1178.
Artículo
9 - Apolinar-Hernandez,M.M., Pena-Ramirez,Y.J., Perez-Rueda,E., Canto-Canche,B.B., De Los Santos-Briones,C., O'Connor-Sanchez,A. (2016). Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatan underground water.
Gene,
593 (1),
154-161.
Artículo
10 - Brambila-Tapia,A.J., Poot-Hernandez,A.C., Perez-Rueda,E., Rodriguez-Vazquez,K. (2016). Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics.
Indian Journal of Microbiology,
56 (2),
134-141.
Artículo
11 - Gama-Castro,S., Salgado,H., Santos-Zavaleta,A., Ledezma-Tejeida,D., Muniz-Rascado,L., Garcia-Sotelo,J.S., Alquicira-Hernandez,K., Martinez-Flores,I., Pannier,L., Castro-Mondragon,J.A., Medina-Rivera,A., Solano-Lira,H., Bonavides-Martinez,C., Perez-Rueda,E., Alquicira-Hernandez,S., Porron-Sotelo,L., Lopez-Fuentes,A., Hernandez-Koutoucheva,A., Moral-Chavez,V.D., Rinaldi,F., Collado-Vides,J. (2016). RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.
Nucleic Acids Research,
44 (D1),
133-143.
Artículo
12 - Martinez-Nunez,M.A., Perez-Rueda,E. (2016). Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?.
Sustainable Chemical Processes,
4 (1),
1-5.
Artículo
13 - Reyes-Perez,A., Vargas,M.D., Hernandez,M., Aguirre-von-Wobeser,E., Perez-Rueda,E., Encarnacion,S. (2016). Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42.
Archives of Microbiology,
198 (9),
847-860.
Artículo
14 - Martinez-Nunez,M.A., Rodriguez-Vazquez,K., Perez-Rueda,E. (2015). The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes.
Proteins: Structure, Function and Bioinformatics,
83 (9),
1625-1631.
Artículo
15 - Ortegon,P., Poot-Hernandez,A.C., Perez-Rueda,E., Rodriguez-Vazquez,K. (2015). Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms.
Computational and Structural Biotechnology Journal,
13,
277-285.
Artículo
16 - Pastor,N., Davila,S., Perez-Rueda,E., Segovia,L., Martinez-Anaya,C. (2015). Electrostatic analysis of bacterial expansins.
Proteins: Structure, Function and Bioinformatics,
83 (2),
215-223.
Artículo
17 - Perez-Rueda,E., Ibarra,J.A. (2015). Distribution of putative xenogeneic silencers in prokaryote genomes.
Computational Biology and Chemistry,
58,
167-172.
Artículo
18 - Perez-Rueda,E., Tenorio-Salgado,S., Huerta-Saquero,A., Balderas-Martinez,Y., Moreno-Hagelsieb,G. (2015). The functional landscape bound to the transcription factors of Escherichia coli K-12.
Computational Biology and Chemistry,
58,
93-103.
Artículo
19 - Poot-Hernandez,A.C., Rodriguez-Vazquez,K., Perez-Rueda,E. (2015). The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria.
BMC Genomics,
16 (1),
957.
Artículo
20 - Armenta-Medina,D., Segovia,L., Perez-Rueda,E. (2014). Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life.
BMC Genomics,
15 (1),
800.
Artículo
21 - Avila-Mendoza,J., Carranza,M., Perez-Rueda,E., Luna,M., Aramburo,C. (2014). Characterization of pituitary growth hormone and its receptor in the green iguana (Iguana iguana).
General and Comparative Endocrinology,
203,
281-295.
Artículo
22 - Brambila-Tapia,A.J., Armenta-Medina,D., Rivera-Gomez,N., Perez-Rueda,E. (2014). Main Functions and Taxonomic Distribution of Virulence Genes in Brucella melitensis 16 M.
PLoS ONE,
9 (6),
e100349.
Artículo
23 - Brambila-Tapia,A.J., Perez-Rueda,E. (2014). A functional and phylogenetic comparison of quorum sensing related genes in Brucella melitensis 16M.
Journal of Microbiology,
52 (8),
709-715.
Artículo
24 - Balderas-Martinez,Y.I., Savageau,M., Salgado,H., Perez-Rueda,E., Morett,E., Collado-Vides,J. (2013). Transcription Factors in Escherichia coli Prefer the Holo Conformation.
PLoS ONE,
8 (6),
e65723.
Artículo
25 - Freyre-Gonzalez,J.A., Manjarrez-Casas,A.M., Merino,E., Martinez-Nunez,M., Perez-Rueda,E., Gutierrez-Rios,R.M. (2013). Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.
BMC Systems Biology,
7 (1),
127.
Artículo
26 - Huerta-Saquero,A., Evangelista-Martinez,Z., Moreno-Enriquez,A., Perez-Rueda,E. (2013). Rhizobium etli asparaginase II: An alternative for acute lymphoblastic leukemia (ALL) treatment.
Bioengineered,
4 (1),
30-36.
Artículo
27 - Ibarra,J.A., Garcia-Zacarias,C.M., Lara-Ochoa,C., Carabarin-Lima,A., Tecpanecatl-Xihuitl,J.S., Perez-Rueda,E., Martinez-Laguna,Y., Puente,J.L. (2013). Further Characterization of Functional Domains of PerA, Role of Amino and Carboxy Terminal Domains in DNA Binding.
PLoS ONE,
8 (2),
e56977.
Artículo
28 - Ibarra,J.A., Perez-Rueda,E., Carroll,R.K., Shaw,L.N. (2013). Global analysis of transcriptional regulators in Staphylococcus aureus.
BMC Genomics,
14 (1),
126.
Artículo
29 - Martinez-Nunez,M.A., Poot-Hernandez,A.C., Rodriguez-Vazquez,K., Perez-Rueda,E. (2013). Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes.
PLoS ONE,
8 (7),
e69707.
Artículo
30 - Tenorio-Salgado,S., Tinoco,R., Vazquez-Duhalt,R., Caballero-Mellado,J., Perez-Rueda,E. (2013). Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens.
Bioengineered,
4 (4).
Artículo
31 - Moreno-Enriquez,A., Evangelista-Martinez,Z., Gonzalez-Mondragon,E.G., Calderon-Flores,A., Arreguin,R., Perez-Rueda,E., Huerta-Saquero,A. (2012). Biochemical Characterization of Recombinant L-Asparaginase (AnsA) from Rhizobium etli, a Member of an Increasing Rhizobial-Type Family of L-Asparaginases.
Journal of Microbiology and Biotechnology,
22 (3),
292-300.
Revisión
32 - Perez-Rueda,E., Martinez-Nunez,M.A. (2012). The repertoire of DNA-binding transcription factors in prokaryotes: functional and evolutionary lessons.
Science Progress,
95 (Pt 3),
315-329.
Artículo
33 - Armenta-Medina,D., Perez-Rueda,E., Segovia,L. (2011). Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches.
Proteins,
79 (5),
1662-1671.
Artículo
34 - Knodler,L.A., Ibarra,J.A., Perez-Rueda,E., Yip,C.K., Steele-Mortimer,O. (2011). Coiled-coil domains enhance the membrane association of Salmonella type III effectors.
Cellular Microbiology,
13 (10),
1497-1517.
Artículo
35 - Rivera-Gomez,N., Segovia,L., Perez-Rueda,E. (2011). The diversity and distribution of TFs and their partner domains play an important role in the regulatory plasticity in bacteria.
Microbiology,
157 (8),
2308-2318.
Artículo
36 - Santos-Zavaleta,A., Gama-Castro,S., Perez-Rueda,E. (2011). A comparative genome analysis of the RpoS-sigmulon shows a high diversity of responses and origins.
Microbiology,
157 (5),
1393-1401.
Revisión
37 - Tenorio-Salgado,S., Huerta-Saquero,A., Perez-Rueda,E. (2011). New insights on gene regulation in archaea.
Computational Biology and Chemistry,
35 (6),
341-346.
Artículo
38 - Chavez-Calvillo,G., Perez-Rueda,E., Lizama,G., Zuniga-Aguilar,J.J., Gaxiola,G., Cuzon,G., Arena-Ortiz,L. (2010). Differential gene expression in Litopenaeus vannamei shrimp in response to diet changes.
Aquaculture,
300 (1-4),
137-141.
Revisión
39 - Martinez-Nunez,M.A., Perez-Rueda,E., Gutierrez-Rios,R.M., Merino,E. (2010). New insights into the regulatory networks of paralogous genes.
Microbiology,
156 (1),
14-22.
Artículo
40 - Perez-Rueda,E., Janga,S.C. (2010). Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.
Molecular Biology And Evolution,
27 (6),
1449-1459.
Artículo
41 - Janga,S.C., Perez-Rueda,E. (2009). Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.
Computational Biology and Chemistry,
33 (4),
261-268.
Revisión
42 - Perez-Rueda,E., Janga,S.C., Martinez-Antonio,A. (2009). Scaling relationship in the gene content of transcriptional machinery in bacteria.
Molecular BioSystems,
5 (12),
1494-1501.
Artículo
43 - Hernandez-Montes,G., Diaz-Mejia,J.J., Perez-Rueda,E., Segovia,L. (2008). The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution.
Genome Biology,
9 (6),
R95.
Artículo
44 - Ibarra,J.A., Perez-Rueda,E., Segovia,L., Puente,J.L. (2008). The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors.
Genetica,
133 (1),
65-76.
Artículo
45 - Sanchez-Flores,A., Perez-Rueda,E., Segovia,L. (2008). Protein homology detection and fold inference through multiple alignment entropy profiles.
Proteins,
70 (1),
248-256.
Artículo
46 - Diaz-Mejia,J.J., Perez-Rueda,E., Segovia,L. (2007). Metabolism evolution by gene duplication: a network perspective.
Genome Biology,
8 (2),
R26.
Artículo
47 - Hernandez-Mendoza,A., Quinto,C., Segovia,L., Perez-Rueda,E. (2007). Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins.
Computational Biology and Chemistry,
31 (2),
115-123.
Artículo
48 - Hernandez-Lucas,I., Ramirez-Trujillo,J.A., Gaitan,M.A., Guo,X., Flores,M., Martinez-Romero,E., Perez-Rueda,E., Mavingui,P. (2006). Isolation and characterization of functional insertion sequences of rhizobia.
Fems Microbiology Letters,
261 (1),
25-31.
Artículo
49 - Moreno-Campuzano,S., Janga,S.C., Perez-Rueda,E. (2006). Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach.
BMC Genomics,
7 (1),
147.
Artículo
50 - Gonzalez,A.D., Espinosa,V., Vasconcelos,A.T., Perez-Rueda,E., Collado-Vides,J. (2005). TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes.
Nucleic Acids Research,
33 (Database Issue),
D98-D102.
Artículo
51 - Perez-Rueda,E., Collado-Vides,J., Segovia,L. (2004). Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.
Computational Biology and Chemistry,
28 (5-6),
341-350.
Internacional
52 - Hernandez-Montes,G., Armenta-Medina,D., Perez-Rueda,E. (2013). Evolution of Metabolism: A Network Perspective of the Amino Acid Biosynthesis Pathways. Encyclopedia of Systems Biology.
687-692.
Nacional
53 - Arena-Ortiz,L., Rojas-Herrera,R., Apodaca-Hernandez,J., Perez-Rueda,E. (2012). Flora Bacteriana en Camarones. Recursos Genéticos Microbianos en la zona Golfo-Sureste de México. Volumen I. .
Internacional
54 - Perez-Rueda,E., Rivera-Gomez,N, Martinez-Nunez,M.A., Tenorio-Salgado,S. (2012). Evolution of DNA-binding Transcription Factors and Regulatory Networks in Prokaryotes. Bacterial Regulatory Networks.
333-346.
Divulgación
55 - Perez-Rueda,E., Santos-Zavaleta,A., Patino-Guerrero,E.A. (2012). Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas?.
Hypatia,
43.
Divulgación
56 - Perez-Rueda,E. (2011). Lo conocido de los desconocidos microbios llamados "Arqueas".
Hypatia,
40.
57 - Perez Rueda, Ernesto (1999). Reconocimiento de motivos estructurales en reguladores transcripcionales.
CIFN,
Doctor en Ciencias (Biologia),
UNAM.
*
Asesor: Collado-Vides, Julio
58 - Perez Rueda, Ernesto (1997). La posicion del motivo de union al DNA como indicador funcional y evolutivo en reguladores transcripcionales .
CIFN,
Maestro en Investigacion Biomedica Basica,
UNAM.
*
Asesor: Collado-Vides, Julio
59 - Perez Rueda, Ernesto (1995). Clasificacion y posibles relaciones funcionales de una coleccion de reguladores transcripcionales de promotores sigma 70 de Escherichia coli .
Facultad de Ciencias,
Licenciatura en Biología,
UNAM.
*
Asesor: Collado-Vides, Julio
Artículo
60 - Avila-Mendoza, J., Perez-Rueda, E., Urban-Sosa, V., Carranza, M., Martinez-Moreno, C.G., Luna, M., Aramburo, C.. Characterization and distribution of GHRH, PACAP, TRH, SST and IGF1 mRNAs in the green iguana.
General and Comparative Endocrinology,
255,
90-101.
Artículo
61 - Flores-Bautista, E., Ludena-Cronick, C., Rodriguez-Fersaca, A., Martinez-Nunez, M.A., Perez-Rueda, E.. Functional prediction of hypothetical transcription factors of Escherichia coli K-12 based on expression data.
Computational and Structural Biotechnology Journal,
16,
157-166.
Artículo
62 - Martinez-Romero, E., Rodriguez-Medina, N., Beltran-Rojel, M., Silva-Sanchez, J., Barrios-Camacho, H., Perez-Rueda, E., Garza-Ramos, U.. Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans.
Salud Publica de Mexico,
60 (1),
56-62.
Artículo
63 - Perez-Rueda, E., Hernandez-Guerrero, R., Martinez-Nunez, M.A., Armenta-Medina, D., Sanchez, I., Ibarra, J.A.. Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.
PLoS ONE,
13 (4),
e0195332.
Artículo
64 - Brambila-Tapia, A.J.L., Perez-Rueda, E., Barrios, H., Davalos-Rodriguez, N.O., Davalos-Rodriguez, I.P., Cardona-Munoz, E.G., Salazar-Paramo, M.. Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach.
Current Microbiology,
74 (8),
915-920.
Artículo
65 - Casella, L.G., Weiss, A., Perez-Rueda, E., Ibarra, J.A., Shaw, L.N.. Towards the complete proteinaceous regulome of Acinetobacter baumannii.
Microbial Genomics,
3 (3),
mgen000107.
Artículo
66 - Martinez-Nunez, M.A., Rodriguez-Escamilla, Z., Rodriguez-Vazquez, K., Perez-Rueda, E.. Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms.
Life (Basel),
7 (3).
Artículo
67 - Rivera-Gomez, N., Martinez-Nunez, M.A., Pastor, N., Rodriguez-Vazquez, K., Perez-Rueda, E.. Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea.
Microbiology,
163 (8),
1167-1178.
Artículo
68 - Apolinar-Hernandez,M.M., Pena-Ramirez,Y.J., Perez-Rueda,E., Canto-Canche,B.B., De Los Santos-Briones,C., O'Connor-Sanchez,A.. Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatan underground water.
Gene,
593 (1),
154-161.
Artículo
69 - Brambila-Tapia,A.J., Poot-Hernandez,A.C., Perez-Rueda,E., Rodriguez-Vazquez,K.. Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics.
Indian Journal of Microbiology,
56 (2),
134-141.
Artículo
70 - Gama-Castro,S., Salgado,H., Santos-Zavaleta,A., Ledezma-Tejeida,D., Muniz-Rascado,L., Garcia-Sotelo,J.S., Alquicira-Hernandez,K., Martinez-Flores,I., Pannier,L., Castro-Mondragon,J.A., Medina-Rivera,A., Solano-Lira,H., Bonavides-Martinez,C., Perez-Rueda,E., Alquicira-Hernandez,S., Porron-Sotelo,L., Lopez-Fuentes,A., Hernandez-Koutoucheva,A., Moral-Chavez,V.D., Rinaldi,F., Collado-Vides,J.. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.
Nucleic Acids Research,
44 (D1),
133-143.
Artículo
71 - Martinez-Nunez,M.A., Perez-Rueda,E.. Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?.
Sustainable Chemical Processes,
4 (1),
1-5.
Artículo
72 - Reyes-Perez,A., Vargas,M.D., Hernandez,M., Aguirre-von-Wobeser,E., Perez-Rueda,E., Encarnacion,S.. Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42.
Archives of Microbiology,
198 (9),
847-860.
Artículo
73 - Martinez-Nunez,M.A., Rodriguez-Vazquez,K., Perez-Rueda,E.. The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes.
Proteins: Structure, Function and Bioinformatics,
83 (9),
1625-1631.
Artículo
74 - Ortegon,P., Poot-Hernandez,A.C., Perez-Rueda,E., Rodriguez-Vazquez,K.. Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms.
Computational and Structural Biotechnology Journal,
13,
277-285.
Artículo
75 - Pastor,N., Davila,S., Perez-Rueda,E., Segovia,L., Martinez-Anaya,C.. Electrostatic analysis of bacterial expansins.
Proteins: Structure, Function and Bioinformatics,
83 (2),
215-223.
Artículo
76 - Perez-Rueda,E., Ibarra,J.A.. Distribution of putative xenogeneic silencers in prokaryote genomes.
Computational Biology and Chemistry,
58,
167-172.
Artículo
77 - Perez-Rueda,E., Tenorio-Salgado,S., Huerta-Saquero,A., Balderas-Martinez,Y., Moreno-Hagelsieb,G.. The functional landscape bound to the transcription factors of Escherichia coli K-12.
Computational Biology and Chemistry,
58,
93-103.
Artículo
78 - Poot-Hernandez,A.C., Rodriguez-Vazquez,K., Perez-Rueda,E.. The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria.
BMC Genomics,
16 (1),
957.
Artículo
79 - Armenta-Medina,D., Segovia,L., Perez-Rueda,E.. Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life.
BMC Genomics,
15 (1),
800.
Artículo
80 - Avila-Mendoza,J., Carranza,M., Perez-Rueda,E., Luna,M., Aramburo,C.. Characterization of pituitary growth hormone and its receptor in the green iguana (Iguana iguana).
General and Comparative Endocrinology,
203,
281-295.
Artículo
81 - Brambila-Tapia,A.J., Armenta-Medina,D., Rivera-Gomez,N., Perez-Rueda,E.. Main Functions and Taxonomic Distribution of Virulence Genes in Brucella melitensis 16 M.
PLoS ONE,
9 (6),
e100349.
Artículo
82 - Brambila-Tapia,A.J., Perez-Rueda,E.. A functional and phylogenetic comparison of quorum sensing related genes in Brucella melitensis 16M.
Journal of Microbiology,
52 (8),
709-715.
Artículo
83 - Balderas-Martinez,Y.I., Savageau,M., Salgado,H., Perez-Rueda,E., Morett,E., Collado-Vides,J.. Transcription Factors in Escherichia coli Prefer the Holo Conformation.
PLoS ONE,
8 (6),
e65723.
Artículo
84 - Freyre-Gonzalez,J.A., Manjarrez-Casas,A.M., Merino,E., Martinez-Nunez,M., Perez-Rueda,E., Gutierrez-Rios,R.M.. Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.
BMC Systems Biology,
7 (1),
127.
Artículo
85 - Huerta-Saquero,A., Evangelista-Martinez,Z., Moreno-Enriquez,A., Perez-Rueda,E.. Rhizobium etli asparaginase II: An alternative for acute lymphoblastic leukemia (ALL) treatment.
Bioengineered,
4 (1),
30-36.
Artículo
86 - Ibarra,J.A., Garcia-Zacarias,C.M., Lara-Ochoa,C., Carabarin-Lima,A., Tecpanecatl-Xihuitl,J.S., Perez-Rueda,E., Martinez-Laguna,Y., Puente,J.L.. Further Characterization of Functional Domains of PerA, Role of Amino and Carboxy Terminal Domains in DNA Binding.
PLoS ONE,
8 (2),
e56977.
Artículo
87 - Ibarra,J.A., Perez-Rueda,E., Carroll,R.K., Shaw,L.N.. Global analysis of transcriptional regulators in Staphylococcus aureus.
BMC Genomics,
14 (1),
126.
Artículo
88 - Martinez-Nunez,M.A., Poot-Hernandez,A.C., Rodriguez-Vazquez,K., Perez-Rueda,E.. Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes.
PLoS ONE,
8 (7),
e69707.
Artículo
89 - Tenorio-Salgado,S., Tinoco,R., Vazquez-Duhalt,R., Caballero-Mellado,J., Perez-Rueda,E.. Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens.
Bioengineered,
4 (4).
Internacional
90 - Hernandez-Montes,G., Armenta-Medina,D., Perez-Rueda,E.. Evolution of Metabolism: A Network Perspective of the Amino Acid Biosynthesis Pathways. Encyclopedia of Systems Biology.
687-692.
Artículo
91 - Moreno-Enriquez,A., Evangelista-Martinez,Z., Gonzalez-Mondragon,E.G., Calderon-Flores,A., Arreguin,R., Perez-Rueda,E., Huerta-Saquero,A.. Biochemical Characterization of Recombinant L-Asparaginase (AnsA) from Rhizobium etli, a Member of an Increasing Rhizobial-Type Family of L-Asparaginases.
Journal of Microbiology and Biotechnology,
22 (3),
292-300.
Revisión
92 - Perez-Rueda,E., Martinez-Nunez,M.A.. The repertoire of DNA-binding transcription factors in prokaryotes: functional and evolutionary lessons.
Science Progress,
95 (Pt 3),
315-329.
Nacional
93 - Arena-Ortiz,L., Rojas-Herrera,R., Apodaca-Hernandez,J., Perez-Rueda,E.. Flora Bacteriana en Camarones. Recursos Genéticos Microbianos en la zona Golfo-Sureste de México. Volumen I. .
Internacional
94 - Perez-Rueda,E., Rivera-Gomez,N, Martinez-Nunez,M.A., Tenorio-Salgado,S.. Evolution of DNA-binding Transcription Factors and Regulatory Networks in Prokaryotes. Bacterial Regulatory Networks.
333-346.
Divulgación
95 - Perez-Rueda,E., Santos-Zavaleta,A., Patino-Guerrero,E.A.. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas?.
Hypatia,
43.
Artículo
96 - Armenta-Medina,D., Perez-Rueda,E., Segovia,L.. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches.
Proteins,
79 (5),
1662-1671.
Artículo
97 - Knodler,L.A., Ibarra,J.A., Perez-Rueda,E., Yip,C.K., Steele-Mortimer,O.. Coiled-coil domains enhance the membrane association of Salmonella type III effectors.
Cellular Microbiology,
13 (10),
1497-1517.
Artículo
98 - Rivera-Gomez,N., Segovia,L., Perez-Rueda,E.. The diversity and distribution of TFs and their partner domains play an important role in the regulatory plasticity in bacteria.
Microbiology,
157 (8),
2308-2318.
Artículo
99 - Santos-Zavaleta,A., Gama-Castro,S., Perez-Rueda,E.. A comparative genome analysis of the RpoS-sigmulon shows a high diversity of responses and origins.
Microbiology,
157 (5),
1393-1401.
Revisión
100 - Tenorio-Salgado,S., Huerta-Saquero,A., Perez-Rueda,E.. New insights on gene regulation in archaea.
Computational Biology and Chemistry,
35 (6),
341-346.
Divulgación
Artículo
102 - Chavez-Calvillo,G., Perez-Rueda,E., Lizama,G., Zuniga-Aguilar,J.J., Gaxiola,G., Cuzon,G., Arena-Ortiz,L.. Differential gene expression in Litopenaeus vannamei shrimp in response to diet changes.
Aquaculture,
300 (1-4),
137-141.
Revisión
103 - Martinez-Nunez,M.A., Perez-Rueda,E., Gutierrez-Rios,R.M., Merino,E.. New insights into the regulatory networks of paralogous genes.
Microbiology,
156 (1),
14-22.
Artículo
104 - Perez-Rueda,E., Janga,S.C.. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.
Molecular Biology And Evolution,
27 (6),
1449-1459.
Artículo
105 - Janga,S.C., Perez-Rueda,E.. Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.
Computational Biology and Chemistry,
33 (4),
261-268.
Revisión
106 - Perez-Rueda,E., Janga,S.C., Martinez-Antonio,A.. Scaling relationship in the gene content of transcriptional machinery in bacteria.
Molecular BioSystems,
5 (12),
1494-1501.
Artículo
107 - Hernandez-Montes,G., Diaz-Mejia,J.J., Perez-Rueda,E., Segovia,L.. The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution.
Genome Biology,
9 (6),
R95.
Artículo
108 - Ibarra,J.A., Perez-Rueda,E., Segovia,L., Puente,J.L.. The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors.
Genetica,
133 (1),
65-76.
Artículo
109 - Sanchez-Flores,A., Perez-Rueda,E., Segovia,L.. Protein homology detection and fold inference through multiple alignment entropy profiles.
Proteins,
70 (1),
248-256.
Artículo
110 - Diaz-Mejia,J.J., Perez-Rueda,E., Segovia,L.. Metabolism evolution by gene duplication: a network perspective.
Genome Biology,
8 (2),
R26.
Artículo
111 - Hernandez-Mendoza,A., Quinto,C., Segovia,L., Perez-Rueda,E.. Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins.
Computational Biology and Chemistry,
31 (2),
115-123.
Artículo
112 - Hernandez-Lucas,I., Ramirez-Trujillo,J.A., Gaitan,M.A., Guo,X., Flores,M., Martinez-Romero,E., Perez-Rueda,E., Mavingui,P.. Isolation and characterization of functional insertion sequences of rhizobia.
Fems Microbiology Letters,
261 (1),
25-31.
Artículo
113 - Moreno-Campuzano,S., Janga,S.C., Perez-Rueda,E.. Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach.
BMC Genomics,
7 (1),
147.
Artículo
114 - Gonzalez,A.D., Espinosa,V., Vasconcelos,A.T., Perez-Rueda,E., Collado-Vides,J.. TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes.
Nucleic Acids Research,
33 (Database Issue),
D98-D102.
Artículo
115 - Perez-Rueda,E., Collado-Vides,J., Segovia,L.. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.
Computational Biology and Chemistry,
28 (5-6),
341-350.
116 - Perez Rueda, Ernesto. Reconocimiento de motivos estructurales en reguladores transcripcionales.
CIFN,
Doctor en Ciencias (Biologia),
UNAM.
*
Asesor: Collado-Vides, Julio
117 - Perez Rueda, Ernesto. La posicion del motivo de union al DNA como indicador funcional y evolutivo en reguladores transcripcionales .
CIFN,
Maestro en Investigacion Biomedica Basica,
UNAM.
*
Asesor: Collado-Vides, Julio
118 - Perez Rueda, Ernesto. Clasificacion y posibles relaciones funcionales de una coleccion de reguladores transcripcionales de promotores sigma 70 de Escherichia coli .
Facultad de Ciencias,
Licenciatura en Biología,
UNAM.
*
Asesor: Collado-Vides, Julio