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.
Open Access 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.
Open Access 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.
Open Access 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.
Open Access 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.
Open Access Artículo
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.
Open Access 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.
Open Access 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
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.
Open Access 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.
Open Access 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.
Open Access 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.
Open Access 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.
Open Access 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
Open Access 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
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.
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.
Open Access 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.
Open Access 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.
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
Open Access 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.
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

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.
Open Access 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.
Open Access 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.
Open Access 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.
Open Access 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.
Open Access Artículo
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.
Open Access 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.
Open Access 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.
Open Access Artículo
Open Access 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.
Open Access Artículo
Open Access 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.
Open Access 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.
Open Access 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.
Open Access Artículo
Open Access Artículo
Internacional
Open Access 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
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
Open Access 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
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
Artículo
Artículo
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.
Open Access 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.
Open Access Artículo
Open Access 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