Mark N. Wass, Gloria Fuentes, Carles Pons, Florencio Pazos and Alfonso Valencia (2011) Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol. 7:469. [PubMed:21326236] [HTML] [PDF]
Poyatos, J. F. (2011) The balance of weak and strong interactions in genetic networks. PLoS ONE, 6, e14598 [PubMed:21347355] [HTML] [PDF]
Martinez-Garcia E, Calles B, Arevalo-Rodriguez M, de Lorenzo V (2011) pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol 11: 38. [PubMed:21342504] [HTML] [PDF]
Monica Chagoyen and Florencio Pazos (2011) MBRole: enrichment analysis of metabolomic data. Bioinformatics.27(5):730-731. [Pubmed:21208985] [HTML] [PDF] [MBROLE server]
Milanesio P, Arce-Rodriguez A, Munoz A, Calles B, de Lorenzo V (2011) Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. Environ Microbiol 13: 324-339. [PubMed:21281420] [HTML] [PDF]
Chavarria M, Santiago C, Platero R, Krell T, Casasnovas JM, et al. (2011) Fructose 1-Phosphate is the preferred effector of the metabolic regulator Cra of Pseudomonas putida. J Biol Chem. [PubMed:21239488] [HTML] [PDF]
Guantes, R., Estrada, J., and Poyatos, J. F. (2010) Trade-offs and noise tolerance in signal detection by genetic circuits. PLoS ONE, 5, 8, e12314. [PubMed:20865033] [HTML] [PDF]
Pfluger-Grau K, Chavarria M, de Lorenzo V (2011) The interplay of the EIIA(Ntr) component of the nitrogen-related phosphotransferase system (PTS(Ntr)) of Pseudomonas putida with pyruvate dehydrogenase. Biochim Biophys Acta. [PubMed:21236318] [HTML]
Zafra O, Fraile S, Gutierrez C, Haro A, Paez-Espino AD, et al. (2011) Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins. Environ Microbiol. [PubMed:21219561] [HTML] [PDF]
de Las Heras A, de Lorenzo V (2011) Cooperative amino acid changes shift the response of the sigma(54) -dependent regulator XylR from natural m-xylene towards xenobiotic 2,4-dinitrotoluene. Mol Microbiol 79: 1248-1259. [PubMed:21205010] [HTML] [PDF]
de Lorenzo V (2011) Genes that move the window of viability of life: lessons from bacteria thriving at the cold extreme: mesophiles can be turned into extremophiles by substituting essential genes. Bioessays 33: 38-42. [PubMed:21072830] [HTML] [PDF]
Koutinas M, Kiparissides A, Silva-Rocha R, Lam MC, Martins Dos Santos VA, et al. (2011) Linking genes to microbial growth kinetics-An integrated biochemical systems engineering approach. Metab Eng. [PubMed:21315172] [HTML]
Koutinas M, Kiparissides A, Lam MC, Silva-Rocha R, Godinho M, de Lorenzo V, Martins Dos Santos VA, Pistikopoulos EN, Mantalaris A. Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid. Biochemical Engineering Journal. 2011.
Silva-Rocha R, Tamames J, Dos Santos VM, de Lorenzo V. The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol. 2011. [PubMed:21410625] [HTML] [PDF]
Zurita E, Chagoyen M, Cantero M, Alonso R, Gonzalez-Neira A, Lopez-Jimenez A, Lopez-Moreno JA, Landel CP, Benitez J, Pazos F, Montoliu L. (2011) Genetic polymorphisms among C57BL/6 mouse inbred strains. Transgenic Res. 20(3):481-489. [Pubmed:20506040] [HTML] [PDF]
Juan C. Triviño and Florencio Pazos. (2010). Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. BMC Syst Biol. 4:46. [Pubmed:20406431] [HTML] [PDF]
de Las Heras A, de Lorenzo V (2010) In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Anal Bioanal Chem. [PubMed:21174197] [HTML] [PDF]
Camas, F. M., Alm, E. J., and Poyatos, J. F. (2010). Local gene regulation details a recognition code within the LacI transcriptional factor family. PLoS Computational Biology, 6, 11, e1000989. [PubMed:21085639] [HTML] [PDF]
de Lorenzo V (2010) Beautiful is not (necessarily) right: overcoming the Phryne's trial syndrome. Bioessays 32: 1011.
David Ochoa and Florencio Pazos. (2010). Studying the co-evolution of protein families with the Mirrortree web server. Bioinformatics. 26(10):1370-1371. [Pubmed:20363731] [HTML] [PDF] [MirrorTree Server] [mirrortree and related programs]
de Lorenzo V (2010) Environmental biosafety in the age of synthetic biology: do we really need a radical new approach? Environmental fates of microorganisms bearing synthetic genomes could be predicted from previous data on traditionally engineered bacteria for in situ bioremediation. Bioessays 32: 926-931. [PubMed:20936643] [HTML] [PDF]
Silva-Rocha R, de Lorenzo V (2010) Noise and robustness in prokaryotic regulatory networks. Annu Rev Microbiol 64: 257-275. [PubMed:20825349] [HTML] [PDF]
Antonio Rausell, David Juan, Florencio Pazos and Alfonso Valencia. (2010). Protein interactions and ligand binding: From protein subfamilies to functional specificity. Proc Natl Acad Sci USA. 107(5):1995-2000. [PubMed:20133844] [HTML] [PDF] [TreeDet server]
Castellon E, Chavarria M, de Lorenzo V, Zayat M, Levy D (2010) An electro-optical device from a biofilm structure created by bacterial activity. Adv Mater 22: 4846-4850. [PubMed:20717993] [HTML] [PDF]
de Las Heras A, Carreno CA, Martinez-Garcia E, de Lorenzo V (2010) Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol Rev 34: 842-865. [PubMed:20618867] [HTML] [PDF]
Koutinas M, Lam MC, Kiparissides A, Silva-Rocha R, Godinho M, et al. (2010) The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environ Microbiol 12: 1705-1718. [PubMed:20553551] [HTML] [PDF]
Monica Chagoyen and Florencio Pazos. (2010). Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data. Bioinformatics. 26(3):378-384. [PubMed:19965879] [HTML] [PDF] [Summary]
Tamames J, de Lorenzo V (2010) EnvMine: a text-mining system for the automatic extraction of contextual information. BMC Bioinformatics 11: 294. [PubMed:20515448] [HTML] [PDF]
de Lorenzo V (2010) Synthetic biology: something old, something new. Bioessays 32: 267-270. [PubMed:20217846] [HTML] [PDF]
Systems Biology Program @CNB-CSIC
c/ Darwin, 3 - 28049 Madrid - Spain
