IBT-UNAM : Dr. Ernesto Perez Rueda
Dr. Ernesto Perez Rueda
Teléfonos
Publicaciones recientes
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.
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, e0195332.
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, 56-62.
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.
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, .
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, 1167-1178.
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, mgen000107.
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, 915-920.
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, 154-161.
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, 847-860.
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, 1-5.
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, 134-141.
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, 133-143.
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, 957.
Perez-Rueda,E. Ibarra,J.A.
2015. Distribution of putative xenogeneic silencers in prokaryote genomes Computational Biology and Chemistry, 58, 167-172.
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, 1625-1631.
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.
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.
Pastor,N. Davila,S. Perez-Rueda,E. Segovia,L. Martinez-Anaya,C.
2015. Electrostatic analysis of bacterial expansins Proteins: Structure, Function and Bioinformatics, 83, 215-223.
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, 800.
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, 709-715.
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, e100349.
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.
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, 127.
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, e69707.
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, e65723 [correction 2013 vol 8 (8)].
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, .
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, e56977.
Ibarra,J.A. Perez-Rueda,E. Carroll,R.K. Shaw,L.N.
2013. Global analysis of transcriptional regulators in Staphylococcus aureus BMC Genomics, 14, 126.
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, 30-36.
Perez-Rueda,E. Martinez-Nunez,M.A.
2012. The repertoire of DNA-binding transcription factors in prokaryotes: functional and evolutionary lessons Science Progress, 95, 315-329.
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, 292-300.
Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda,E.
2011. New insights on gene regulation in archaea Computational Biology and Chemistry, 35, 341-346.
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, 1497-1517.
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, 2308-2318.
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, 1662-1671.
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, 1393-1401.
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, 137-141.
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, 1449-1459.
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, 14-22.
Perez-Rueda,E. Janga,S.C. Martinez-Antonio,A.
2009. Scaling relationship in the gene content of transcriptional machinery in bacteria Molecular BioSystems, 5, 1494-1501.
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, 261-268.
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, R95.
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, 65-76.
Sanchez-Flores,A. Perez-Rueda,E. Segovia,L.
2008. Protein homology detection and fold inference through multiple alignment entropy profiles Proteins, 70, 248-256.
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, 115-123.
Diaz-Mejia,J.J. Perez-Rueda,E. Segovia,L.
2007. Metabolism evolution by gene duplication: a network perspective Genome Biology, 8, R26.
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, 25-31.
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, 147.
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, D98-D102.
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, 341-350.
Salgado,H. Santos-Zavaleta,A. Gama-Castro,S. Millen-Zarate,D. Diaz-Peredo,E. Sanchez-Solano,F. Perez-Rueda,E. Bonavides-Martinez,C. Collado-Vides,J.
2001. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 Nucleic Acids Research, 29, 72-74 * .
Moreno-Hagelsieb,G. Trevino,V. Perez-Rueda,E. Smith,T.F. Collado-Vides,J.
2001. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli Trends in Genetics, 17, 175-177 * .
Perez-Rueda,E. Collado-Vides,J.
2001. Common history at the origin of the position-function correlation in transcriptional regulators in Archaea and Bacteria Journal of Molecular Evolution, 53, 172-179 * .
Perez-Rueda,E. Collado-Vides,J.
2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12 Nucleic Acids Research, 28, 1838-1847 * .
Perez-Rueda,E. Gralla.JD Collado-Vides,J.
1998. Genomic position analyses and the transcription machinery Journal of Molecular Biology, 275, 165-170 * .
Thieffry,D. Huerta,A.M. Perez-Rueda,E. Collado-Vides,J.
1998. 3.0.CO;2-2> From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli Bioessays, 20, 433-440 * .
Hernandez-Montes,G. Armenta-Medina,D. Perez-Rueda,E. 2013. Evolution of Metabolism: A Network Perspective of the Amino Acid Biosynthesis Pathways en: Dubitzky,W. Encyclopedia of Systems Biology. Springer. pags. 687-692
Arena-Ortiz,L. Rojas-Herrera,R. Apodaca-Hernandez,J. Perez-Rueda,E. 2012. Flora Bacteriana en Camarones en: Rojas,R. Recursos Genéticos Microbianos en la zona Golfo-Sureste de México. Volumen I.
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 en: Filloux,A.A.M. Bacterial Regulatory Networks. Caister Academic Press. pags. 333-346
Collado-Vides,J. Moreno-Hagelsieb,G. Perez-Rueda,E. 2002. 5 en: Hofestadt,R. Gene regulation and metabolism : postgenomic computational approaches. MIT Press. pags. 103-128 *
Otras Publicaciones Perez-Rueda,E. Santos-Zavaleta,A. Patino-Guerrero,E.A.
2012. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas? Hypatia, 43, .
Perez-Rueda,E.
2011. Lo conocido de los desconocidos microbios llamados "Arqueas". Hypatia, 40, .
* Indica publicación con otra institución de adscripción
ex-colaborador y/o ex-alumno