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| ==Contact Info==
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| [[Image:OWWEmblem.png|thumb|right|Ernesto Perez-Rueda (an artistic interpretation)]]
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| *Universidad Nacional Autonoma de Mexico
| | This site is in development. Please see our IIMAS - UNAM [http://www.iimas.unam.mx homepage], the Encyclopedia of well-known Transcription Factors in Bacteria and Archaea: '''ENTRAF Database''' [http://web.pcyt.unam.mx/EntrafDB], '''Gene Regulatory Network server (GRN)'''[https://regulatorynetworks.unam.mx] or [http://132.247.46.6], and '''CDBPROM''' [https://aw.iimas.unam.mx/cdbprom] |
| *Avenida Universidad 1001, Col. Chamilpa
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| *Cuernavaca, Morelos, Mexico
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| *Email address: [[erueda@ibt.unam.mx]]
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| *'''Facebook''' : Laboratorio de Biologia Computacional [http://www.facebook.com/pages/Laboratorio-de-Biologia-Computacional/139885586119371]
| | [[Image: Ernesto_Perez-Rueda lab_orig.png|300px]] |
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| *'''Google Scholar''' : Publications and citations [https://scholar.google.com/citations?hl=en&user=H5fCIIgAAAAJ&view_op=list_works&gmla=AJsN-F6OrAVigGjli3pF68u1xuUSkZmE0OA7xyIuN9xH6pcLpF2nwhTxz1JZVC2a5Si5Gxd8geV4OSHNOlJXerBpju7W4mSsZXV01PzGCOZvH87YAF-DJLG1C3tq_2BSBIn7WFHZFPAi]
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| *'''Blog''' : Group Blog [http://labcomputationalbiology.blogspot.mx]
| | <div style="padding: 10px; color: #ffffff; background-color: #000; width: 730px"> |
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| *'''Publications''': Publications at NCBI [http://www.ncbi.nlm.nih.gov/pubmed/?term=perez-rueda%20e]
| | [[Ernesto-Perez-Rueda:Contact | <font face="trebuchet ms" style="color:#ffffff"> '''Contact''' </font>]] |
| | [[Ernesto-Perez-Rueda:Education | <font face="trebuchet ms" style="color:#ffffff"> '''Education''' </font>]] |
| | [[Ernesto-Perez-Rueda:Lab Members / Research interests | <font face="trebuchet ms" style="color:#ffffff"> '''Lab Members''' </font>]] |
| | [[Ernesto-Perez-Rueda:Publications | <font face="trebuchet ms" style="color:#ffffff"> '''Publications''' </font>]] |
| | [[Ernesto-Perez-Rueda :Book Chapters | <font face="trebuchet ms" style="color:#ffffff"> '''Book Chapters''' </font>]] |
| | [[Ernesto-Perez-Rueda :Dissemination | <font face="trebuchet ms" style="color:#ffffff"> '''Dissemination''' </font>]] |
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| I work in the "''Instituto de Biotecnologia''[http://www.ibt.unam.mx]" at ''Universidad Nacional Autonoma de Mexico[http://www.unam.mx]''. I have interest on Gene Regulation, Genomics, Evolution of metabolism, and Bioinformatics.
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| ==Education==
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| * 1999, PhD Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [http://www.ccg.unam.mx], UNAM
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| * 1997, MS Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [http://www.ccg.unam.mx], UNAM
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| * 1995, BS Biology, Facultad de Ciencias[http://www.fciencias.unam.mx/], UNAM
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| | =Welcome= |
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| ==Lab Members / Research interests==
| | Welcome to the Laboratory of Computational Biology at Merida, Yucatan. Mexico [https://en.wikipedia.org/wiki/M%C3%A9rida,_Yucat%C3%A1n] |
| <!-- Feel free to add brief descriptions to your research interests as well -->
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| #'''Aniel Brambila Tapia''' / Postdoctoral research / Comparative Genomics.
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| # Nancy Rivera Gomez / Postdoctoral research / [http://www.ibt.unam.mx/server/PRG.base?tipo:doc,dir:PRG.curriculum,par:nrivera]/ Gene Regulation, Evolution
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| # Dagoberto Armenta Medina [http://www.ibt.unam.mx/server/PRG.base?tipo:doc,dir:PRG.curriculum,par:darmenta] / Evolution of metabolism
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| # Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
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| # Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics
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| ==Publications==
| | We are centered on understanding gene regulation and metabolism including computational approaches. In this regard, our work on Gene regulation involves the analysis of DNA-binding transcription factors in Archaea and Bacteria cellular domains. Our approach considers the identification of TFs by the design of family-specific HMM models and by the search with models deposited in diverse databases. We have identified and evaluated the repertories of TFs in three bacterial models: '''Escherichia coli K12''' [https://en.wikipedia.org/wiki/Escherichia_coli], '''Bacillus subtilis 168''' [https://en.wikipedia.org/wiki/Bacillus_subtilis] and '''Staphylococcus aureus''' [https://en.wikipedia.org/wiki/Staphylococcus_aureus]. |
| <!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed -->
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| 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. [http://www.sciencedirect.com/science/article/pii/S2001037015000203]
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| | In addition, we explore the use of network approaches to analyze the evolution of metabolism. From this perspective and using large-scale genomic and bioinformatics tools, eleven different amino acid pathways have been proposed as ancestral to bacteria, archaea, and eukarya, closer to the last common ancestor. We also suggested that Metabolic Pathways have evolved by the recruitment of blocks of enzymes sharing similar catalytic activities. |
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| 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. [http://onlinelibrary.wiley.com/doi/10.1002/prot.24718/abstract]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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 [http://www.biomedcentral.com/1752-0509/7/127/abstract]
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| 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. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069707]
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| 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 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0065723]
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| 31. Ibarra JA, '''Perez-Rueda,E''', Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [http://www.biomedcentral.com/1471-2164/14/126/abstract]
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| 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. [http://www.landesbioscience.com/journals/bioe/article/23808]
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| 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. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056977].
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| 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). [https://www.landesbioscience.com/journals/bioe/article/21710/]
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| 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. [http://www.ingentaconnect.com/content/stl/sciprg/2012/00000095/00000003/art00005?token=005b1e49bc2a53709bc35f7e2a46762c6b635d76766c257b3a446c24673f7b2f267738703375686f4919ff0787f]
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| 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. [http://www.jmb.or.kr/journal/paper_view.html?book=&tops=&start=0&scale=15&key=&key_word=&Vol=&Num=&PG=&year1=&year2=&sort=&aut_box=&sub_box=&sos_box=&key_box=&pub_box=&abs_box=&mod=&mnum=3975]
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| 25. Tenorio-Salgado,S. Huerta-Saquero,A. '''Perez-Rueda,E'''. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[http://www.sciencedirect.com/science/article/pii/S1476927111001083].
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| 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.[http://dx.doi.org/10.1111/j.1462-5822.2011.01635.x].
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| 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.[http://mic.sgmjournals.org/content/early/2011/06/01/mic.0.050617-0].
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| 22. Santos-Zavaleta A, Gama-Castro MS, '''Perez-Rueda,E'''. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [http://mic.sgmjournals.org/cgi/content/abstract/mic.0.042937-0v1?maxtoshow=&hits=10&RESULTFORMAT=&author1=perez-rueda&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT].
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| 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. [http://onlinelibrary.wiley.com/doi/10.1002/prot.22995/abstract].
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| 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. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T4D-4XVK3V4-3&_user=945819&_coverDate=02%2F27%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000048981&_version=1&_urlVersion=0&_userid=945819&md5=3afaf8039b74fbf069d7ef53fc018b43&searchtype=a|]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=20123795]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=19850620]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=19763344]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=19632156]
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| 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.[http://www.ncbi.nlm.nih.gov/pubmed/?term=18541022]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=17712603]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=17671981]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=17416336]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=17326820]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=16842354]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=16772031]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608293]
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| 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 [http://www.ncbi.nlm.nih.gov/pubmed/?term=15556475]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=11523004]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=11275307]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125053]
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| 3. '''Perez-Rueda E,''' Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [http://www.ncbi.nlm.nih.gov/pubmed/?term=10734204]
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| 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. [http://www.ncbi.nlm.nih.gov/pubmed/?term=9670816]
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| 1. '''Perez-Rueda E,''' Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [http://www.ncbi.nlm.nih.gov/pubmed/?term=9466899]
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| == Book Chapters ==
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| 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.
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| 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. [http://www.horizonpress.com/regulatorynetworks]
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| 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. [http://www.springerreference.com/docs/html/chapterdbid/308964.html]
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| 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.
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| ==Dissemination==
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| 2. '''Perez-Rueda E''', Santos-Zavaleta A. Patino-Guerrero EA. 2012. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas? Hypatia, 43. [http://hypatia.morelos.gob.mx/index.php?option=com_content&task=view&id=843&Itemid=814] ''In spanish''.
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| 1. '''Perez-Rueda E''' 2011. Lo conocido de los desconocidos microbios llamados “Arqueas”. Hypatia. [http://hypatia.morelos.gob.mx/index.php?option=com_content&task=view&id=713&Itemid=657]. ''In spanish''.
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| ==Useful links==
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| *[[OpenWetWare:Welcome|Introductory tutorial]]
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| *[[Help|OpenWetWare help pages]]
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| *[[http://www.ibt.unam.mx| Instituto de Biotecnologia, UNAM]]
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