User:Ernesto Perez-Rueda: Difference between revisions
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39. Pastor N, Dávila, '''Perez-Rueda,E''', Segovia L, Martínez-Anaya. 2014. Electrostatic analysis of bacterial expansins. DOI: 10.1002/prot.24718 [http://onlinelibrary.wiley.com/doi/10.1002/prot.24718/abstract] | |||
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. [http://www.biomedcentral.com/1471-2164/15/800/abstract] | |||
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. [http://www.sciencedirect.com/science/article/pii/S0016648014001397] | |||
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. [http://link.springer.com/article/10.1007/s12275-014-3570-x] | |||
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. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0100349] | |||
Revision as of 14:42, 15 November 2014
Contact Info
- Universidad Nacional Autonoma de Mexico
- Avenida Universidad 1001, Col. Chamilpa
- Cuernavaca, Morelos, Mexico
- Email address: erueda@ibt.unam.mx
- Facebook : Laboratorio de Biologia Computacional [1]
- ResearcherID : Publications and citations [2]
- Blog : Group Blog [3]
I work in the "Instituto de Biotecnologia[4]" at Universidad Nacional Autonoma de Mexico[5]. I have interest on Gene Regulation, Genomics, Evolution of metabolism, and Bioinformatics.
Education
- 1999, PhD Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [6], UNAM
- 1997, MS Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [7], UNAM
- 1995, BS Biology, Facultad de Ciencias[8], UNAM
Lab Members / Research interests
- Aniel Brambila Tapia / Postdoctoral research / Comparative Genomics.
- Nancy Rivera Gomez / Postdoctoral research / [9]/ Gene Regulation, Evolution
- Dagoberto Armenta Medina [10] / Evolution of metabolism
- Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
- Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics
Publications
39. Pastor N, Dávila, Perez-Rueda,E, Segovia L, Martínez-Anaya. 2014. Electrostatic analysis of bacterial expansins. DOI: 10.1002/prot.24718 [11]
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. [12]
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. [13]
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. [14]
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. [15]
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 [16]
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. [17]
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 [18]
31. Ibarra JA, Perez-Rueda,E, Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [19]
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. [20]
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. [21].
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). [22]
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. [23]
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. [24]
25. Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda,E. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[25].
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.[26].
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.[27].
22. Santos-Zavaleta A, Gama-Castro MS, Perez-Rueda,E. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [28].
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. [29].
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. [30]
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. [31]
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. [32]
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. [33]
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. [34]
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.[35]
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. [36]
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. [37]
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. [38]
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. [39]
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. [40]
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. [41]
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. [42]
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 [43]
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. [44]
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. [45]
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. [46]
3. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [47]
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. [48]
1. Perez-Rueda E, Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [49]
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. [50]
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. [51]
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
2. Perez-Rueda E, Santos-Zavaleta A. Patino-Guerrero EA. 2012. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas? Hypatia, 43. [52] In spanish.
1. Perez-Rueda E 2011. Lo conocido de los desconocidos microbios llamados “Arqueas”. Hypatia. [53]. In spanish.
