User:Ernesto Perez-Rueda: Difference between revisions

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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]


''''''== 2013 ==''''''


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. In press.
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]




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]
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]




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. In press.[http://www.landesbioscience.com/journals/bioe/article/23808/]
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]




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].
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]




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/]
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]




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.
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]




''''''== 2012 ==''''''
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]


'''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]


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].


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]


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/]


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]


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]


'''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]


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]


'''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''.




''''''== 2011 ==''''''
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].




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].
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].




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].
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].




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].
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].




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].
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].




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].
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|]




'''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''.
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]




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]


''''''== 2010 ==''''''


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]


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|]


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]


'''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]


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]


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]


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]


''''''== 2009 ==''''''


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]


'''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]


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]


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]


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]


''''''== 2008 ==''''''


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]


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]


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]


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]


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]


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]


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]


''''''== 2007 ==''''''


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]


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]


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]


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]


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]


''''''== 2006 ==''''''


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]


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]


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]


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]


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]


''''''== 2005 ==''''''
== Book Chapters ==




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]
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.




''''''== 2004 ==''''''
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]




'''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]
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]




''''''== 2002 ==''''''
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==


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.


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''.


''''''== 2001 ==''''''


 
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''.
'''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]
 
 
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]
 
 
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]
 
 
''''''== 2000 ==''''''
 
 
'''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]
 
 
 
''''''== 1998 ==''''''
 
 
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]
 
 
'''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]


==Useful links==
==Useful links==

Revision as of 09:42, 3 September 2014

Contact Info

Ernesto Perez-Rueda (an artistic interpretation)
  • 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

  1. Aniel Brambila Tapia / Postdoctoral research / Comparative Genomics.
  2. Nancy Rivera Gomez / Postdoctoral research / [9]/ Gene Regulation, Evolution
  3. Dagoberto Armenta Medina [10] / Evolution of metabolism
  4. Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
  5. Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics

Publications

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. [11]


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. [12]


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. [13]


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 [14]


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. [15]


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 [16]


31. Ibarra JA, Perez-Rueda,E, Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [17]


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. [18]


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. [19].


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). [20]


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. [21]


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. [22]


25. Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda,E. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[23].


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.[24].


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.[25].


22. Santos-Zavaleta A, Gama-Castro MS, Perez-Rueda,E. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [26].


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. [27].


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. [28]


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. [29]


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. [30]


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. [31]


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. [32]


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.[33]


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. [34]


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. [35]


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. [36]


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. [37]


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. [38]


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. [39]


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. [40]


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 [41]


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. [42]


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. [43]


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. [44]


3. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [45]


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. [46]


1. Perez-Rueda E, Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [47]

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. [48]


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. [49]


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. [50] In spanish.


1. Perez-Rueda E 2011. Lo conocido de los desconocidos microbios llamados “Arqueas”. Hypatia. [51]. In spanish.

Useful links

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