User:Ernesto Perez-Rueda
Contact Info
- Universidad Nacional Autonoma de Mexico
- Avenida Universidad 1001, Col. Chamilpa
- Cuernavaca, Morelos, Mexico
- Email address: erueda@ibt.unam.mx
- Sistema Nacional de Investigadores : Nivel 3.
- New site : Laboratory of Computational Biology [1]
- Facebook : Laboratorio de Biologia Computacional [2]
- Google Scholar : Publications and citations [3]
- Blog : Group Blog [4]
I work in the "Instituto de Biotecnologia[7]" at Universidad Nacional Autonoma de Mexico[8]. I have interest on Gene Regulation, Genomics, Evolution of metabolism, and Bioinformatics.
Education
- 1999, PhD Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [9], UNAM
- 1997, MS Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [10], UNAM
- 1995, BS Biology, Facultad de Ciencias[11], UNAM
Lab Members / Research interests
- Aniel Brambila Tapia / Postdoctoral research / Comparative Genomics.
- Nancy Rivera Gomez / Postdoctoral research / [12]/ Gene Regulation, Evolution
- Dagoberto Armenta Medina [13] / Evolution of metabolism
- Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
- Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics
Publications
53. Rivera-Gomez N, Martinez-Nuñez MA, Pastor N, Rodriguez-Vazquez K, Perez-Rueda E. 2017. Dissecting the Protein Architecture of DNA-Binding Transcription Factors in Bacteria and Archaea. Microbiology. Aceptado.
52. Martínez-Romero E, Rodriguez-Medina N, Beltrán-Rojel M, Silva-Sanchez J, Barrios-Camacho H, Perez-Rueda E, Garza-Ramos U. 2017. Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans. Salud Pública de México. In press.
51. Brambila-Tapia, AJL, Perez-Rueda E, Barrios B, Dávalos-Rodríguez NO, Dávalos-Rodríguez IP, Cardona-Muñoz EG, Salazar-Páramo M. 2017. Identification of beta-lactamases and beta-lactam related proteins in human pathogenic bacteria by comparative proteomics. Current Microbiology. [14]
50. Casella LG, Weiss A, Perez-Rueda E, Ibarra JA, Shaw LN. 2017. Towards the Complete Proteinaceous Regulome of Acinetobacter baumannii. Microbial Genomics. [15]
49. Apolinar–Hernández MM, Peña–Ramírez YJ, Perez-Rueda E, Canto-Canché BB, Santos-Briones C, O'Connor-Sánchez A. 2016. Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water. Gene 593(1):154–161. [16]
48. Reyes-Perez A, Vargas MC, 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. [17]
47. Brambila-Tapia, AJL, Poot-Hernandez CA, 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. [18]
46.Martinez-Nuñez MA, Perez-Rueda E. 2016. Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?. Sustainable Chemical Processes. 4:3. [19].
45. Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo J, Alquicira-Hernández K, Martínez-Flores I, Pannier, L, Castro-Mondragón J, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Perez-Rueda E, Alquicira-Hernández S; Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, del Moral-Chávez V, 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):D133-D143. [20]
44. Poot-Hernandez CA, 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 [21].
43. Perez-Rueda E, Ibarra JA. 2015. Distribution of putative xenogeneic silencers in prokaryote genomes. Computational Biology and Chemistry. 58:167-172. [22]
42. Martinez-Nuñez MA, Rodriguez-Vazquez K, Perez-Rueda E. 2015 “The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes. Proteins: Structure, Function, and Bioinformatics. In press. [23]
41. Perez-Rueda E, Tenorio-Salgado,S, Huerta-Saquero A, Balderas-Martinez Y, Moreno-Hagelsieb. 2015. The functional landscape bound to the transcription factors of Escherichia coli K-12. Computational Biology and Chemistry. 6;58:93-103. [24]
- Comment on Atlas of Science: Escherichia coli K-12 as a model to understand gene regulation. 2015. [25].
40. Ortegon P, Poot-Hernandez AC, Perez-Rueda E, Rodríguez-Vazquez K, . 2015. Comparison of metabolic pathways in Escherichia coli by using genetic algorithms. Computational and Structural Biotechnology Journal, 13, 277-285. [26]
39. Pastor N, Dávila, Perez-Rueda E, Segovia L, Martínez-Anaya. 2015. Electrostatic analysis of bacterial expansins. Proteins: Structure, Function, and Bioinformatics, 83, 215-223. [27]
38. 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. [28]
37. 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. [29]
36. Brambila-Tapia, AJL, Perez-Rueda E. 2014. A functional and phylogenetic comparison of Quorum Sensing related genes in Brucella melitensis 16M. Journal of Microbiology. 52, 709-715. [30]
35. Brambila-Tapia, AJL, Armenta-Medina D, Rivera-Gomez N, Perez-Rueda E. 2014. Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16M. PLoS ONE, 9, e100349. [31]
34. Freyre-González JA, Manjarrez-Casas AM, Merino E, Martinez-Nuñez MA, Perez-Rueda E, Gutiérrez-Ríos RM. Lessons from he modular organization of the transcriptional regulatory network of Bacillus subtilis. BMC Systems Biology 2013, 7:127 [32]
33. Martinez-Nuñez MA, Poot-Hernandez AC, Rodríguez-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. [33]
32. Balderas-Martínez YI, 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 [34]
31. Ibarra JA, Perez-Rueda E, Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [35]
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):1–8. [36]
29. Ibarra JA, García-Zacarias CM, Lara-Ochoa C, Carabarin-Lima A, Tecpanecatl S, Perez-Rueda E, Martínez-Laguna Y, Puente JL. 2013. Further characterization of functional domains of PerA, role of amino and carboxy terminal domains in DNA binding. PLoS ONE 8(2): e56977. [37].
28. Huerta-Saquero A, Evangelista-Martínez Z, Moreno-Enriquez A,Perez-Rueda E. 2013. Rhizobium etli asparaginase II: An alternative for acute lymphoblastic leukemia (ALL) treatment. Bioengineered. 4(1). [38]
27. Perez-Rueda E, Martinez-Nuñez M.A. 2012. The Repertoire of DNA-Binding Transcription Factors in Prokaryotes: Functional and Evolutionary Lessons. Science Progress. 95:315-329. [39]
26. Moreno-Enriquez, A. Evangelista-Martínez, Z. González-Mondragón, E. 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. J. Microbiol. Biotechnol. 22:292–300. [40]
25. Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda E. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[41].
24. Knodler, L. Ibarra, JA.Perez-Rueda E. Yip, C, Steele-Mortimer O. 2011. Coiled-coils domains enhance the membrane association of Salmonella type II effectors. Cellular Microbiology, 13, 1497-1517.[42].
23. 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.[43].
22. Santos-Zavaleta A, Gama-Castro MS, Perez-Rueda E. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [44].
21. 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. [45].
20. 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. [46]
19. Perez-Rueda E. Janga,S.C. 2010. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin Mol Biol Evol. 27, 1449-1459. [47]
18. 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. [48]
17. Perez-Rueda E. Janga,S.C. Martinez-Antonio,A. 2009. Scaling relationship in the gene content of transcriptional machinery in bacteria Mol Biosystems, 5, 1494-1501. [49]
16. Janga,S.C. Perez-Rueda E. 2009. Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families Comput Biol Chem, 33, 261-268. [50]
15. 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 Biol, 9, R95.[51]
14. 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. [52]
13. Sanchez-Flores,A. Perez-Rueda E. Segovia,L. 2008. Protein homology detection and fold inference through multiple alignment entropy profiles PROTEINS: Structure, Function, and Bioinformatics, 70, 248-256. [53]
12. Hernandez-Mendoza,A. Quinto,C. Segovia,L. Perez-Rueda E. 2007. Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins Comput. Biol Chem, 31, 115-123. [54]
11. Diaz-Mejia,J.J. Perez-Rueda E. Segovia,L. 2007. A network perspective on the evolution of metabolism by gene duplication. Genome Biol, 8, R26. [55]
10. 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 Microbiol.Lett., 261, 25-31. [56]
9. Moreno-Campuzano,S. Chandra,J.S. 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. [57]
8. Gonzalez AD, Espinosa V, Vasconcelos AT, Perez-Rueda E, Collado-Vides J. 2005. TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Research.33, 98-102. [58]
7. Perez-Rueda E, Collado-Vides J, Segovia L. 2004. Phylogenetic Distribution of DNA-binding Transcription Factors in Bacteria and Archaea A genomic approach. Computational Biology and Chemistry. 28, 341-350 [59]
6. 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. [60]
5. Moreno-Hagelsieb G, Treviño V, Perez-Rueda E, Smith T, Collado-Vides J. 2001 Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends in Genetics. 17,175-177. [61]
4. Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zárate 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 K12. Nucleic Acids Research. 29, 72-74. [62]
3. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [63]
2. Thieffry, D. Huerta AM, Perez-Rueda E, Collado-Vides J. 1998. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. BioEssays, 20:1-8. [64]
1. Perez-Rueda E, Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [65]
Book Chapters
4. Arena-Ortiz, L. Rojas-Herrera, R. Apodaca-Hernandez, J. Perez-Rueda E. 2013. Flora Bacteriana en Camarones. En Recursos Genéticos Microbianos en la zona Golfo-Sureste de México. Volumen I. Editores M. Gamboa, R. Rojas. In press.
3. Perez-Rueda, E. Rivera-Gomez, N. Martinez-Nunez, MA. Tenorio-Salgado, S. 2012. Evolution of DNA-binding Transcription Factors and Regulatory Networks in Prokaryotes in: Evolution of regulatory networks in bacteria Horizon Scientific Press. [66]
2. Hernández-Montes, G. Armenta-Medina, D. Perez-Rueda, E. 2012. Evolution of metabolism: A network perspective of the amino acid biosynthesis pathways. Encyclopedia of Systems Biology. Springer. [67]
1. Collado-Vides J, Moreno-Hagelsieb G, Perez-Rueda, E. et al. 2002 Genomics of Gene Regulation: The view from Escherichia coli in: Gene Regulation and Metabolism: Post-Genomic Computational Approaches eds. Collado-Vides J. and Hofestadt R. MIT Press.
Dissemination
3. Escherichia coli K-12 as a model to understand gene regulation. 2015. Atlas of Science. [68].
2. Perez-Rueda E, Santos-Zavaleta A. Patino-Guerrero EA. 2012. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas? Hypatia, 43. [69] In spanish.
1. Perez-Rueda E 2011. Lo conocido de los desconocidos microbios llamados “Arqueas”. Hypatia. [70]. In spanish.
