Ernesto-Perez-Rueda:Publications

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62. Galan-Vasquez E and Perez-Rueda E. 2019. Identification of modules with similar gene regulation and metabolic functions based on co-expression. Frontiers in Molecular Biosciences.[1]


61. Castelán-Sánchez HG, Elorrieta P, Romoacca P, Liñan-Torres A, Sierra JL, Ingrid Vera I, Batista-García RA, Tenorio-Salgado S, Lizama-Uc G, Perez-Rueda E, Quispe-Ricalde MA, Sonia Dávila-Ramos S. 2019. Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses. Genes. 10(11), 891. [2]


60. Escobar-Turriza P, Hernández-Guerrero R, Poot-Hernández AC, Rodríguez-Vázquez K, Ramírez-Prado J, Perez-Rueda E. 2019. Identification of functional signatures in the metabolism of the three cellular domains of life. PLoS One 14(5): e0217083. [3].


59. Santos-Zavaleta A, Perez-Rueda E, Sánchez-Pérez M, Velázquez-Ramírez D, Collado-Vides J. 2019. Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes. BMC Genomics. 20, 299 [4]


58. Denis A, Martínez-Núñez MA, Tenorio-Salgado S, Perez-Rueda E. 2018. Dissecting the repertoire of DNA-binding Transcription factor of the archaeon Pyrococcus furiosus DSM 3638. Life, 8, 40. [5]


57. Perez-Rueda E, Hernandez-Guerrero R, Martinez-Nuñez MA, Armenta-Medina D, Sanchez I, Ibarra JA. 2018. Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. PLoS One. 13(4):e0195332. [6]


56. Flores-Bautista E, Ludeña C, Rodriguez A, Martínez-Núñez MA, 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. [7]


55. Martínez-Romero E, Rodriguez-Medina N, Beltrán-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 Pública de México. 60, 56-62. [8]


54. Ávila-Mendoza, Perez-Rueda E, Urban-Sosa V, Carranza M, Martínez-Moreno CG, Luna M, Arámburo C. 2018. Characterization and distribution of GHRH, PACAP, TRH, SST and IGF1 mRNAs in the green iguana. General and Comparative Endocrinology. 255:90-101. [9]


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. 163:1167-1178. [10].


52. Martinez-Nuñez MA, Rodriguez-Escamilla Z, Rodríguez-Vazquez K, Perez-Rueda E. 2017. Tracing the repertoire of promiscuous enzymes along the metabolic pathways in archaeal organisms. Life. 7:30. [11]


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, 74:915-920. [12]


50. Casella LG, Weiss A, Perez-Rueda E, Ibarra JA, Shaw LN. 2017. Towards the Complete Proteinaceous Regulome of Acinetobacter baumannii. Microbial Genomics. [13]


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 593:154–161. [14]


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. 198:847–860. [15]


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. [16]


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. [17].


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. [18]


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 [19].


43. Perez-Rueda E, Ibarra JA. 2015. Distribution of putative xenogeneic silencers in prokaryote genomes. Computational Biology and Chemistry. 58:167-172. [20]


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. 83:1625–1631. [21]


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. 58:93-103. [22]

  • Comment on Atlas of Science: Escherichia coli K-12 as a model to understand gene regulation. 2015. [23].


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. [24]


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. [25]


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. [26]


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. [27]


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. [28]


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. [29]


34. Freyre-González JA, Manjarrez-Casas AM, Merino E, Martinez-Nuñez MA, Perez-Rueda E, Gutiérrez-Ríos RM. 2013. Lessons from he modular organization of the transcriptional regulatory network of Bacillus subtilis. BMC Systems Biology 7:127 [30]


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. [31]


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 [32]


31. Ibarra JA, Perez-Rueda E, Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics. 14:126. [33]


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. [34]


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: e56977. [35].


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). [36]


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. [37]


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. [38]


25. Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda E. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[39].


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.[40].


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.[41].


22. Santos-Zavaleta A, Gama-Castro MS, Perez-Rueda E. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [42].


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. [43].


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. [44]


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. [45]


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. [46]


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. [47]


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. [48]


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.[49]


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. [50]


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. [51]


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. [52]


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. [53]


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. [54]


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. [55]


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. [56]


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 [57]


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. [58]


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. [59]


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. [60]


3. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [61]


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. [62]


1. Perez-Rueda E, Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [63]