2020
Martin AJ,, Perez-Rueda E, Garrido D. 2020. Editorial: Systems Modeling: Approaches and Applications. Frontiers in Molecular Biosciences. 7:620464. [1]
González-Torres I, Perez-Rueda E Evangelista-Martínez Z, Zárate-Romero A, Moreno-Enriquez A, Huerta-Saquero A. 2020. Selection of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles. A bioinformatic approach. PeerJ 8:e10276. [2].
Castelán-Sánchez HG, Meza-Rodríguez PM, Carrillo E, Ríos-Vázquez DI, Liñan-Torres A, Batista-García RA, Perez-Rueda E, Rojas-Ruíz NE, Dávila-Ramos S. 2020. The microbial composition in circumneutral thermal springs from Chignahuapan, Puebla, Mexico reveals the presence of particular sulfur-oxidizing bacterial and viral communities. Microorganisms. 8(11):1677.[3]
Lenz AR, Galan-Vasquez E, Balbinot E, Abreu FP, Souza de Oliveira N, Rosa LO, de Avila e Silva S, Camassola M, Dillon AJP, Perez-Rueda E. 2020. Gene regulatory networks of Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 inferred by a computational biology approach. Frontiers in Microbiology. 11:588263. [4]
Flores-Bautista E, Hernandez-Guerrero R, Huerta-Saquero A, Tenorio-Salgado S, Rivera-Gomez N, Romero A, Ibarra JA, Perez-Rueda E. 2020. Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms. PLoS One. 15(8): e0237135. [5]
Sanchez I. Hernández-Guerrero R, Mendez-Monroy PE, Martinez-Nunez MA, Ibarra JA and Perez-Rueda E. 2020. Evaluation of abundance of DNA-binding transcription factors in prokaryotes. Genes. 11(1), 52. [6
González-Torres I, Perez-Rueda E Evangelista-Martínez Z, Zárate-Romero A, Moreno-Enriquez A, Huerta-Saquero A. 2020. Selection of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles. A bioinformatic approach. PeerJ 8:e10276. [2].
Castelán-Sánchez HG, Meza-Rodríguez PM, Carrillo E, Ríos-Vázquez DI, Liñan-Torres A, Batista-García RA, Perez-Rueda E, Rojas-Ruíz NE, Dávila-Ramos S. 2020. The microbial composition in circumneutral thermal springs from Chignahuapan, Puebla, Mexico reveals the presence of particular sulfur-oxidizing bacterial and viral communities. Microorganisms. 8(11):1677.[3]
Lenz AR, Galan-Vasquez E, Balbinot E, Abreu FP, Souza de Oliveira N, Rosa LO, de Avila e Silva S, Camassola M, Dillon AJP, Perez-Rueda E. 2020. Gene regulatory networks of Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 inferred by a computational biology approach. Frontiers in Microbiology. 11:588263. [4]
Flores-Bautista E, Hernandez-Guerrero R, Huerta-Saquero A, Tenorio-Salgado S, Rivera-Gomez N, Romero A, Ibarra JA, Perez-Rueda E. 2020. Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms. PLoS One. 15(8): e0237135. [5]
Sanchez I. Hernández-Guerrero R, Mendez-Monroy PE, Martinez-Nunez MA, Ibarra JA and Perez-Rueda E. 2020. Evaluation of abundance of DNA-binding transcription factors in prokaryotes. Genes. 11(1), 52. [6
2019
Hernández-Guerrero R, Galan-Vasquez E and Perez-Rueda E. 2019. The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains. PLoS One. 14(12):e0226604. [2].
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.[3]
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. [4]
Sánchez-Domínguez I, Monroy PEM, Perez-Rueda E. 2019. Prototype of a Multivariable Measurement System. In: González Díaz C. et al. (eds) VIII Latin American Conference on Biomedical Engineering. [5]
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. 99 [12]
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 [13]
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.[3]
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. [4]
Sánchez-Domínguez I, Monroy PEM, Perez-Rueda E. 2019. Prototype of a Multivariable Measurement System. In: González Díaz C. et al. (eds) VIII Latin American Conference on Biomedical Engineering. [5]
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. 99 [12]
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 [13]
2018
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. [14]
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. [15]
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. [16]
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. [15]
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. [. [17]
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. [15]
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. [16]
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. [15]
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. [. [17]
2017 - 1998
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. [16].
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. [15]
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]
Casella LG, Weiss A, Perez-Rueda E, Ibarra JA, Shaw LN. 2017. Towards the Complete Proteinaceous Regulome of Acinetobacter baumannii. Microbial Genomics. [12]
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. [13].
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. [14].
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. [15]
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. [16].
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. [17]
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 [18].
Perez-Rueda E, Ibarra JA. 2015. Distribution of putative xenogeneic silencers in prokaryote genomes. Computational Biology and Chemistry. 58:167-172. [19]
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. [20]
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. [21]
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. [23]
Pastor N, Dávila, Perez-Rueda E Segovia L, Martínez-Anaya. 2015. Electrostatic analysis of bacterial expansins. Proteins: Structure, Function, and Bioinformatics, 83, 215-223. [24]
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. [25]
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. [26]
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. [27]
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. [28]
Freyre-González JA, et al. Lessons from he modular organization of the transcriptional regulatory network of Bacillus subtilis. BMC Systems Biology 2013, 7:127 [29]
Martinez-Nuñez MA, et al 2013. Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes. PLoS ONE. 8(7): e69707. [30]
Balderas-Martínez YI, et al 2013. Transcription factors in Escherichia coli prefer the holo conformation. PLoS ONE. 8(6): e65723 [31]
Ibarra JA, et al. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [32]
Tenorio-Salgado S, et al. 2013. Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens. Bioengineered. 4(4):1–8. [33]
Ibarra JA, et al. 2013. Further characterization of functional domains of PerA, role of amino and carboxy terminal domains in DNA binding. PLoS ONE 8(2): e56977. [34].
Huerta-Saquero A, et al 2013. Rhizobium etli asparaginase II: An alternative for acute lymphoblastic leukemia (ALL) treatment. Bioengineered. 4(1). [35]
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. [36]
Moreno-Enriquez, A. et al. 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. [37]
Tenorio-Salgado,S. et al. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[38].
Knodler, L. et al. 2011. Coiled-coils domains enhance the membrane association of Salmonella type II effectors. Cellular Microbiology, 13, 1497-1517.[39].
Rivera-Gomez,N. et al 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.[40].
Santos-Zavaleta A, et al. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [41].
Armenta-Medina, D. et al. 2011. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches Proteins, 79, 1662-1671. [42].
Chavez-Calvillo,G. et al. 2010. Differential gene expression in Litopenaeus vannamei shrimp in response to diet changes. Aquaculture, 300, 137-141. [43]
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. [44]
Martinez-Nunez,M.A. et al. 2010. New insights into the regulatory networks of paralogous genes Microbiology, 156, 14-22. [45]
Perez-Rueda E,. et al 2009. Scaling relationship in the gene content of transcriptional machinery in bacteria Mol Biosystems, 5, 1494-1501. [46]
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. [47]
Hernandez-Montes,G. et al. 2008. The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution Genome Biol, 9, R95.[48]
Ibarra,J.A. et al 2008. The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors Genetica, 133, 65-76. [49]
Sanchez-Flores,A. et al. 2008. Protein homology detection and fold inference through multiple alignment entropy profiles PROTEINS: Structure, Function, and Bioinformatics, 70, 248-256. [50]
Hernandez-Mendoza,A. et al. 2007. Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins Comput. Biol Chem, 31, 115-123. [51]
Diaz-Mejia,J.J. et al. 2007. A network perspective on the evolution of metabolism by gene duplication. Genome Biol, 8, R26. [52]
Hernandez-Lucas,I. et al. 2006. Isolation and characterization of functional insertion sequences of rhizobia FEMS Microbiol.Lett., 261, 25-31. [53]
Moreno-Campuzano,S. et al. 2006. Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach BMC Genomics, 7, 147. [54]
Gonzalez AD, et al. 2005. TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Research.33, 98-102. [55]
Perez-Rueda E,, et al. 2004. Phylogenetic Distribution of DNA-binding Transcription Factors in Bacteria and Archaea A genomic approach. Computational Biology and Chemistry. 28, 341-350 [56]
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. [57]
Moreno-Hagelsieb G, et al. 2001 Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends in Genetics. 17,175-177. [58]
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. [59]
Perez-Rueda E,, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [60]
Thieffry, D. et al. 1998. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. BioEssays, 20:1-8. [61]
Perez-Rueda E,, et al. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [62]
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. [15]
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]
Casella LG, Weiss A, Perez-Rueda E, Ibarra JA, Shaw LN. 2017. Towards the Complete Proteinaceous Regulome of Acinetobacter baumannii. Microbial Genomics. [12]
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. [13].
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. [14].
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. [15]
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. [16].
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. [17]
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 [18].
Perez-Rueda E, Ibarra JA. 2015. Distribution of putative xenogeneic silencers in prokaryote genomes. Computational Biology and Chemistry. 58:167-172. [19]
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. [20]
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. [21]
- Comment on Atlas of Science: Escherichia coli K-12 as a model to understand gene regulation. 2015. [22].
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. [23]
Pastor N, Dávila, Perez-Rueda E Segovia L, Martínez-Anaya. 2015. Electrostatic analysis of bacterial expansins. Proteins: Structure, Function, and Bioinformatics, 83, 215-223. [24]
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. [25]
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. [26]
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. [27]
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. [28]
Freyre-González JA, et al. Lessons from he modular organization of the transcriptional regulatory network of Bacillus subtilis. BMC Systems Biology 2013, 7:127 [29]
Martinez-Nuñez MA, et al 2013. Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes. PLoS ONE. 8(7): e69707. [30]
Balderas-Martínez YI, et al 2013. Transcription factors in Escherichia coli prefer the holo conformation. PLoS ONE. 8(6): e65723 [31]
Ibarra JA, et al. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [32]
Tenorio-Salgado S, et al. 2013. Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens. Bioengineered. 4(4):1–8. [33]
Ibarra JA, et al. 2013. Further characterization of functional domains of PerA, role of amino and carboxy terminal domains in DNA binding. PLoS ONE 8(2): e56977. [34].
Huerta-Saquero A, et al 2013. Rhizobium etli asparaginase II: An alternative for acute lymphoblastic leukemia (ALL) treatment. Bioengineered. 4(1). [35]
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. [36]
Moreno-Enriquez, A. et al. 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. [37]
Tenorio-Salgado,S. et al. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[38].
Knodler, L. et al. 2011. Coiled-coils domains enhance the membrane association of Salmonella type II effectors. Cellular Microbiology, 13, 1497-1517.[39].
Rivera-Gomez,N. et al 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.[40].
Santos-Zavaleta A, et al. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [41].
Armenta-Medina, D. et al. 2011. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches Proteins, 79, 1662-1671. [42].
Chavez-Calvillo,G. et al. 2010. Differential gene expression in Litopenaeus vannamei shrimp in response to diet changes. Aquaculture, 300, 137-141. [43]
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. [44]
Martinez-Nunez,M.A. et al. 2010. New insights into the regulatory networks of paralogous genes Microbiology, 156, 14-22. [45]
Perez-Rueda E,. et al 2009. Scaling relationship in the gene content of transcriptional machinery in bacteria Mol Biosystems, 5, 1494-1501. [46]
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. [47]
Hernandez-Montes,G. et al. 2008. The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution Genome Biol, 9, R95.[48]
Ibarra,J.A. et al 2008. The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors Genetica, 133, 65-76. [49]
Sanchez-Flores,A. et al. 2008. Protein homology detection and fold inference through multiple alignment entropy profiles PROTEINS: Structure, Function, and Bioinformatics, 70, 248-256. [50]
Hernandez-Mendoza,A. et al. 2007. Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins Comput. Biol Chem, 31, 115-123. [51]
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