User:Ernesto Perez-Rueda

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*Cuernavaca, Morelos, Mexico  
*Cuernavaca, Morelos, Mexico  
*Email address: [[erueda@ibt.unam.mx]]
*Email address: [[erueda@ibt.unam.mx]]
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*'''Sistema Nacional de Investigadores''' : '''''Nivel 3'''''.
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*'''New site''' : Laboratory of Computational Biology [http://computationalbiology.weebly.com]
*'''Facebook''' : Laboratorio de Biologia Computacional [http://www.facebook.com/pages/Laboratorio-de-Biologia-Computacional/139885586119371]
*'''Facebook''' : Laboratorio de Biologia Computacional [http://www.facebook.com/pages/Laboratorio-de-Biologia-Computacional/139885586119371]
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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]
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*'''Publications''': Publications  at NCBI [http://www.ncbi.nlm.nih.gov/pubmed/?term=perez-rueda%20e] and at Europe PMC [https://europepmc.org/search?query=perez-rueda+e&page=1&sortby=Date]
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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.
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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<!-- Feel free to add brief descriptions to your research interests as well -->
<!-- Feel free to add brief descriptions to your research interests as well -->
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#'''Aniel Brambila Tapia''' / Postdoctoral research / Comparative Genomics --> '''New member'''.
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#'''Aniel Brambila Tapia''' / Postdoctoral research / Comparative Genomics.
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# Nancy Rivera Gomez [http://www.ibt.unam.mx/server/PRG.base?tipo:doc,dir:PRG.curriculum,par:nrivera]/ Gene Regulation, Evolution
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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
# Dagoberto Armenta Medina [http://www.ibt.unam.mx/server/PRG.base?tipo:doc,dir:PRG.curriculum,par:darmenta] / Evolution of metabolism
# Dagoberto Armenta Medina [http://www.ibt.unam.mx/server/PRG.base?tipo:doc,dir:PRG.curriculum,par:darmenta] / Evolution of metabolism
# Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
# Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
# Cesar Poot Hernandez  / Evolution of metabolism, Bioinformatics
# Cesar Poot Hernandez  / Evolution of metabolism, Bioinformatics
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# Mashenka Garcia Saiz  / Pathogenesis, Genomics
 
==Publications==
==Publications==
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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. In press.  
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51. Brambila-Tapia, AJL, '''Perez-Rueda E''', Barrios B, Dávalos-Rodríguez NO, Dávalos-Rodríguez IP, Cardona-Muñoz EG, Salazar-Páramo M. 2017. Identification of beta-lactamases and beta-lactam related proteins in human pathogenic bacteria by comparative proteomics. Current Microbiology. [https://link.springer.com/article/10.1007%2Fs00284-017-1265-3]
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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. In press.[http://www.landesbioscience.com/journals/bioe/article/23808/]
 
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50.      Casella LG, Weiss A,  '''Perez-Rueda E''', Ibarra JA, Shaw LN. 2017. Towards the Complete Proteinaceous Regulome of Acinetobacter baumannii. Microbial Genomics. [http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000107]
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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. In press.
 
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49.    Apolinar–Hernández MM, Peña–Ramírez YJ, '''Perez-Rueda E''', Canto-Canché BB, Santos-Briones C, O'Connor-Sánchez A. 2016. Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water. Gene 593(1):154–161. [http://www.sciencedirect.com/science/article/pii/S0378111916306254]
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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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48. Reyes-Perez A, Vargas MC, Hernandez M, Aguirre-von-Wobeser E, '''Perez-Rueda E''', Encarnacion S. 2016. Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42. Archives of Microbiology. 198(9):847–860. [http://link.springer.com/article/10.1007/s00203-016-1241-5]
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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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47. Brambila-Tapia, AJL, Poot-Hernandez CA, '''Perez-Rueda E''', Rodriguez-Vazquez K. 2016. Identification of DNA methyltransferase genes in human pathogenic bacteria by comparative genomics. Indian Journal of Microbiology, 56, 134-141. [http://link.springer.com/article/10.1007/s12088-015-0562-4?wt_mc=internal.event.1.SEM.ArticleAuthorOnlineFirst]
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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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46.Martinez-Nuñez MA, '''Perez-Rueda E'''. 2016. Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?. Sustainable Chemical Processes. 4:3. [http://sustainablechemicalprocesses.springeropen.com/articles/10.1186/s40508-016-0047-8].
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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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'''''A more detailed explanation about the archaeal TFs role is described.'''''
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45. Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo J, Alquicira-Hernández K, Martínez-Flores I, Pannier, L, Castro-Mondragón J, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, '''Perez-Rueda E''', Alquicira-Hernández S; Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, del Moral-Chávez V, Rinaldi F, Collado-Vides J. 2016. RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering, and beyond. Nucleic Acids Research. 44(D1):D133-D143. [http://dx.doi.org/10.1093/nar/gkv1156]
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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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44. Poot-Hernandez CA, Rodriguez-Vazquez K, '''Perez-Rueda E'''. 2015. The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria. BMC Genomics. 16:957 [http://www.biomedcentral.com/1471-2164/16/957].
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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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43. '''Perez-Rueda E''', Ibarra JA. 2015. Distribution of putative xenogeneic silencers in prokaryote genomes. Computational Biology and Chemistry. 58:167-172. [http://www.sciencedirect.com/science/article/pii/S147692711530058X]
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'''''We evaluate the repertoire of winged helix-turn-helix domains (wHTHs), a class of DNA-binding TFs in bacterial sequence genomes. The repertoire of wHTHs in terms of their partner domains, or PaDos was evaluated. Based on the PaDos, we defined three main groups of families: i) monolithic, those families with little diversity of PaDos, such as LysR; ii) promiscuous, those families with a high diversity of PaDos; iii) monodomain, with families of small sizes, such as MarR. These findings suggest that PaDos have a very important role in the diversification of regulatory responses in bacteria, probably contributing to their regulatory complexity.'''''
 
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42. Martinez-Nuñez MA, Rodriguez-Vazquez K, '''Perez-Rueda E'''. 2015 “The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes. Proteins: Structure, Function, and Bioinformatics. In press. [http://onlinelibrary.wiley.com/doi/10.1002/prot.24847/abstract]
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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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41. '''Perez-Rueda E''', Tenorio-Salgado,S, Huerta-Saquero A, Balderas-Martinez Y, Moreno-Hagelsieb. 2015. The functional landscape bound to the transcription factors of Escherichia coli K-12. Computational Biology and Chemistry. 6;58:93-103. [http://www.sciencedirect.com/science/article/pii/S1476927115300232]
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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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* Comment on Atlas of Science: Escherichia coli K-12 as a model to understand gene regulation. 2015. [http://atlasofscience.org/escherichia-coli-model-gene].
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''''' In this work we used an integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), to identify evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family.'''''
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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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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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*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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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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'''''We propose that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could form different combinations of monomers similar to that observed in eukaryotic transcriptional machinery.'''''
 
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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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*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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'''''Our survey reinforces the notion that despite TFs being the most prominent components shaping the regulatory networks, other elements are also important. These include small RNAs, riboswitches, RNA-binding proteins, sigma factors, protein-protein interactions and DNA supercoiling, which modulate the expression of genes involved in particular metabolic processes or induce a more complex response in terms of the regulatory networks of paralogous genes in an integrated interplay with TFs'''''
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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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*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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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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'''''Here, we show that sigma, transcription factors (TFs) and the number of protein coding genes occur in different magnitudes across 291 non-redundant eubacterial genomes. Clustering of the distribution of transcription and sigma families across genomes suggests that functional constraints could force their co-evolution, as was observed in sigma54, IHF and EBP families.'''''
 
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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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*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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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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*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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'''''We predicted a core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids, suggesting that this core occurred in ancient cells, before the separation of the three cellular domains of life. The distribution of two types of alternative branches to this core: analogs, enzymes that catalyze the same reaction (using the same metabolites) and belong to different superfamilies is described; and 'alternologs', herein defined as branches that, proceeding via different metabolites, converge to the same end product'''''
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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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*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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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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'''''In this work, using the DNA binding domain of 58 experimentally characterized proteins from the AraC/XylS (A/X), 1974 A/X proteins were found in 149 out of 212 bacterial genomes. This domain was used as a template to generate a phylogenetic tree and as a tool to predict the putative regulatory role of the new members of this family based on their proximity to a particular functional cluster in the tree'''''
 
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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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*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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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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*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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'''''AcrB of Escherichia coli was used to predict the compounds transported by 47 RND proteins, based on 14 amino acids directly involved in substrate interactions. These residues provide enough information to identify 16 groups that correlates with the ligand they extrude, such as proteins expelling aromatic hydrocarbons or proteins expelling heavy metals'''''
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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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*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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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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'''''This work shows that metabolic networks have a high retention of duplicates within functional modules, and a preferential biochemical coupling of reactions. A high retention of duplicates between chemically similar reactions, as illustrated by fatty-acid metabolism, was also identified. The retention of duplicates between chemically dissimilar reactions is, however, also greater than expected by chance'''''
 
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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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*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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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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*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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'''''A collection of 237 DNA-binding Transcription Factors (TFs) was identified in B. subtilis. 59% of them were predicted to be repressors, 17% activators, 17% were putatively identified as dual regulatory proteins and the remaining 6.3% could not be associated with a regulatory role. 56 TFs were found to be autoregulated, most of them negatively, though a significant proportion of positive feedback circuits were also identified. In addition, six global regulators were defined in B. subtilis based on the number and function of their regulated genes.'''''
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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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*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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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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*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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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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*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]
+
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].
-
*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]
+
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].
-
*4. '''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]
+
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|]
-
'''''A total of 314 regulatory DNA-binding proteins was identified in Escherichia coli, which might represent its minimal set of transcription factors. The collection is comprised of 35% activators, 43% repressors and 22% dual regulators. This work describes a full characterization of the repertoire of regulatory interactions in a whole living cell.'''''
 
 +
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]
-
*3. 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]
 
 +
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]
-
*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]
 
 +
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]
-
*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]
 
-
'''''In bacteria and eukaryotes, regulatory proteins are found to have their DNA-binding domains near termini.'''''
+
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]
-
==Book Chapters==
 
-
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
 
-
*4. 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]
+
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
 
 +
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]
 +
 
 +
== 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. [http://www.horizonpress.com/regulatorynetworks]
 +
 
 +
 
 +
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]
 +
 
 +
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.
-
*3. Arena-Ortiz, L. Rojas-Herrera, R. Apodaca-Hernandez, J. '''Perez-Rueda E.''' 2012 Flora Bacteriana en Camarones. En Recursos Genéticos Microbianos en la zona Golfo-Sureste de México. Volumen I. Editores M. Gamboa, R. Rojas. In press.
+
==Dissemination==
-
*2. '''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]
+
3. Escherichia coli K-12 as a model to understand gene regulation. 2015. Atlas of Science. [http://atlasofscience.org/escherichia-coli-model-gene].
-
*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.
+
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''.
-
==Papers of 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. [http://hypatia.morelos.gob.mx/index.php?option=com_content&task=view&id=843&Itemid=814] ''In spanish''.
 
-
*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''.
+
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''.
==Useful links==
==Useful links==

Current revision

Contents

Contact Info

Ernesto Perez-Rueda (an artistic interpretation)
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


  • Sistema Nacional de Investigadores : Nivel 3.


  • New site : Laboratory of Computational Biology [1]
  • Facebook : Laboratorio de Biologia Computacional [2]
  • Google Scholar : Publications and citations [3]
  • Blog : Group Blog [4]
  • Publications: Publications at NCBI [5] and at Europe PMC [6]


I work in the "Instituto de Biotecnologia[7]" at Universidad Nacional Autonoma de Mexico[8]. I have interest on Gene Regulation, Genomics, Evolution of metabolism, and Bioinformatics.

Education

  • 1999, PhD Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [9], UNAM
  • 1997, MS Biomedical Sciences, Centro de Investigacion Sobre Fijacion de Nitrogeno [10], UNAM
  • 1995, BS Biology, Facultad de Ciencias[11], UNAM


Lab Members / Research interests

  1. Aniel Brambila Tapia / Postdoctoral research / Comparative Genomics.
  2. Nancy Rivera Gomez / Postdoctoral research / [12]/ Gene Regulation, Evolution
  3. Dagoberto Armenta Medina [13] / Evolution of metabolism
  4. Patricia Ortegon Cano / Evolution of metabolism, Genetic algorithms design
  5. Cesar Poot Hernandez / Evolution of metabolism, Bioinformatics

Publications

51. Brambila-Tapia, AJL, Perez-Rueda E, Barrios B, Dávalos-Rodríguez NO, Dávalos-Rodríguez IP, Cardona-Muñoz EG, Salazar-Páramo M. 2017. Identification of beta-lactamases and beta-lactam related proteins in human pathogenic bacteria by comparative proteomics. Current Microbiology. [14]


50. Casella LG, Weiss A, Perez-Rueda E, Ibarra JA, Shaw LN. 2017. Towards the Complete Proteinaceous Regulome of Acinetobacter baumannii. Microbial Genomics. [15]


49. Apolinar–Hernández MM, Peña–Ramírez YJ, Perez-Rueda E, Canto-Canché BB, Santos-Briones C, O'Connor-Sánchez A. 2016. Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water. Gene 593(1):154–161. [16]


48. Reyes-Perez A, Vargas MC, Hernandez M, Aguirre-von-Wobeser E, Perez-Rueda E, Encarnacion S. 2016. Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42. Archives of Microbiology. 198(9):847–860. [17]


47. Brambila-Tapia, AJL, Poot-Hernandez CA, Perez-Rueda E, Rodriguez-Vazquez K. 2016. Identification of DNA methyltransferase genes in human pathogenic bacteria by comparative genomics. Indian Journal of Microbiology, 56, 134-141. [18]


46.Martinez-Nuñez MA, Perez-Rueda E. 2016. Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?. Sustainable Chemical Processes. 4:3. [19].


45. Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo J, Alquicira-Hernández K, Martínez-Flores I, Pannier, L, Castro-Mondragón J, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Perez-Rueda E, Alquicira-Hernández S; Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, del Moral-Chávez V, Rinaldi F, Collado-Vides J. 2016. RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering, and beyond. Nucleic Acids Research. 44(D1):D133-D143. [20]


44. Poot-Hernandez CA, Rodriguez-Vazquez K, Perez-Rueda E. 2015. The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria. BMC Genomics. 16:957 [21].


43. Perez-Rueda E, Ibarra JA. 2015. Distribution of putative xenogeneic silencers in prokaryote genomes. Computational Biology and Chemistry. 58:167-172. [22]


42. Martinez-Nuñez MA, Rodriguez-Vazquez K, Perez-Rueda E. 2015 “The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes. Proteins: Structure, Function, and Bioinformatics. In press. [23]


41. Perez-Rueda E, Tenorio-Salgado,S, Huerta-Saquero A, Balderas-Martinez Y, Moreno-Hagelsieb. 2015. The functional landscape bound to the transcription factors of Escherichia coli K-12. Computational Biology and Chemistry. 6;58:93-103. [24]

  • Comment on Atlas of Science: Escherichia coli K-12 as a model to understand gene regulation. 2015. [25].


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. [26]


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. [27]


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. [28]


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. [29]


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. [30]


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. [31]


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 [32]


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. [33]


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 [34]


31. Ibarra JA, Perez-Rueda E, Carroll RK, Shaw LN. 2013. Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics, 14:126. [35]


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. [36]


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. [37].


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). [38]


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. [39]


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. [40]


25. Tenorio-Salgado,S. Huerta-Saquero,A. Perez-Rueda E. 2011. New insights on gene regulation in archaea. Comput. Biol. Chem. 35, 341-346.[41].


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.[42].


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.[43].


22. Santos-Zavaleta A, Gama-Castro MS, Perez-Rueda E. 2011. A comparative genome analysis of the RpoS Sigmulon. Microbiology, 157, 1393-1401. [44].


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. [45].


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. [46]


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. [47]


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. [48]


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. [49]


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. [50]


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.[51]


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. [52]


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. [53]


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. [54]


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. [55]


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. [56]


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. [57]


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. [58]


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 [59]


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. [60]


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. [61]


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. [62]


3. Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847. [63]


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. [64]


1. Perez-Rueda E, Gralla J, Collado-Vides J. 1998. Genomic Position Analysis and the Transcription Machinery. Journal of Molecular Biology. 27,165-170. [65]

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. [66]


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. [67]


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

3. Escherichia coli K-12 as a model to understand gene regulation. 2015. Atlas of Science. [68].


2. Perez-Rueda E, Santos-Zavaleta A. Patino-Guerrero EA. 2012. Lo que hay detrás de las biopelículas bacterianas ¿perjudiciales o benéficas? Hypatia, 43. [69] In spanish.


1. Perez-Rueda E 2011. Lo conocido de los desconocidos microbios llamados “Arqueas”. Hypatia. [70]. In spanish.

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