Journal articles: 2013 - 2012 - 2011 - 2010
de Juan D, Pazos F, Valencia A (2013) Emerging methods in protein co-evolution. Nat Rev Genetics. 14(4): 249-61. [PubMed:23458856] [HTML] [PDF] [more info and available tools]
Cavaliere M, Poyatos JF (2013) Plasticity facilitates sustainable growth in the commons. Journal of the Royal Society Interface, 10(81):20121006. [PubMed:23365195]
Tamames J, Durante-Rodríguez G (2013) Taxonomy becoming a driving force in genome sequencing projects. Syst Appl Microbiol. 2013 Feb 28. [PubMed:23453737]
López-López A, Richter M, Peña A, Tamames J, Rosselló-Móra R (2013) New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach. Syst Appl Microbiol. 2013 Jan 23. [PubMed:23352736]
Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, Gallego JL, Bargiela R, López-López A, Pieper DH, Rosselló-Móra R, Sánchez J, Seifert J, Ferrer M (2013) Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. ISME J. 7(1):122-36. [PubMed:22832345] [PubMed Central:PMC3526184]
Pietrosemoli N, García-Martín JA, Solano R, Pazos F (2013) Genome-Wide Analysis of Protein Disorder in Arabidopsis thaliana: Implications for Plant Environmental Adaptation. PLoS One. 8(2):e55524. [PubMed:23408995]
Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F (2013) Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. Molecular Biosystems. 9(1):70-76. [PubMed:23104128] [Mirrortree and related programs] [Mirrortree web server]
Silva-Rocha R, Pérez-Pantoja D, de Lorenzo V (2013) Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2. ISME J. 7(2):229-32. [PubMed:22895160] [PubMed Central:PMC3554407]
Nikel PI, de Lorenzo V (2013) Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors. J Biotechnol. 163(2):143-54. [PubMed:22609234]
de Lorenzo V, Pieper D, Ramos JL (2013) From the test tube to the environment - and back. Environ Microbiol. 15(1):6-11. [PubMed:23286645]
Silva-Rocha R, de Lorenzo V (2013) The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Environ Microbiol. 15(1):271-86. [PubMed:23171249]
Chavarría M, Fuhrer T, Sauer U, Pflüger-Grau K, de Lorenzo V (2013) Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate : phosphotransferase system of Pseudomonas putida. Environ Microbiol. 15(1):121-32. [PubMed:22708906]
Silva-Rocha R, Chavarría M, Kleijn RJ, Sauer U, de Lorenzo V (2013) The IHF regulon of exponentially growing Pseudomonas putida cells. Environ Microbiol. 15(1):49-63. [PubMed:22510163]
Nikel PI, de Lorenzo V (2013) Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. Metab Eng. 15:98-112. [PubMed:23149123]
Silva-Rocha R, Martínez-García E, Calles B, Chavarría M, Arce-Rodríguez A, de Las Heras A, Páez-Espino AD, Durante-Rodríguez G, Kim J, Nikel PI, Platero R, de Lorenzo V (2013) The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res. 41(Database issue):D666-75. [PubMed:23180763] [PubMed Central:PMC3531073]
Bajic D. and Poyatos JF (2012) Balancing noise and plasticity in gene expression. BMC Genomics 13:343. [PubMed:22839658] [PubMed Central:PMC3539894]
Poyatos JF (2012) On the search for design principles in biological systems. Adv Exp Med Biol. 751:183-93. [PubMed:22821459]
Natalia Pietrosemoli, Daniel Lopez, Aldo Segura-Cabrera and Florencio Pazos (2012) Computational Prediction of Important Regions in Protein Sequences. IEEE Signal Processing Magazine. 29(6):143-147. [HTML] [PDF] [Xdet and other tools] [JDet software]
Chagoyen M, Pazos F (2012). Tools for the functional interpretation of metabolomic experiments. Briefings in Bioinformatics. [PubMed:23063930] [HTML] [list of tools]
Muth T, García-Martín JA, Rausell A, Juan D, Valencia A, Pazos F (2012) JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics. 28(4):584-586. [PubMed:22171333] [HTML] [JDet software]
Chavarría M, Nikel PI, Pérez-Pantoja D, de Lorenzo V. (2012)The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol. [PubMed:23301697]
Tamames J, Rosselló-Móra R (2012) On the fitness of microbial taxonomy. Trends Microbiol. 20(11):514-6. [PubMed:22959411]
de Lorenzo V (2012)Towards a global biotechnology scenario. Curr Opin Biotechnol. 23(6):827-9. [PubMed:23178194]
Silva-Rocha R, de Lorenzo V (2012) Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene. Mol Microbiol. 2012 Oct;86(1):199-211. [PubMed:22845424]
Jurado P, Fernández LA, de Lorenzo V (2012) Production and characterization of a recombinant single-chain antibody (scFv) for tracing the σ54 factor of Pseudomonas putida. J Biotechnol. 160(1-2):33-41. [PubMed:22206981]
Schmidt M, de Lorenzo V (2012) Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett. 586(15):2199-206. [PubMed:22710182] [PubMed Central:PMC3396840]
Silva-Rocha R, de Lorenzo V (2012) Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor. Mol Biosyst.8(7):1950-7. [PubMed:22588473]
Leprince A, de Lorenzo V, Völler P, van Passel MW, Martins dos Santos VA (2012) Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol. 14(6):1444-53. [PubMed:22429517] [PubMed Central:PMC3429869]
Chavarría M, Kleijn RJ, Sauer U, Pflüger-Grau K, de Lorenzo V (2012) Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. MBio. 3(2). [PubMed:22434849] [PubMed Central:PMC3312210]
Arce-Rodríguez A, Durante-Rodríguez G, Platero R, Krell T, Calles B, de Lorenzo V (2012) The Crp regulator of Pseudomonas putida: evidence of an unusually high affinity for its physiological effector, cAMP. Environ Microbiol. (3):702-13. [PubMed:22040086]
de Las Heras A, de Lorenzo V (2012) Engineering whole-cell biosensors with no antibiotic markers for monitoring aromatic compounds in the environment. Methods Mol Biol. 834:261-81. [PubMed:22144365]
Martínez-García E, de Lorenzo V (2012) Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria. Methods Mol Biol. 813:267-83. [PubMed:22083748]
Leprince A, Janus D, de Lorenzo V, Santos VM (2012) Streamlining of a Pseudomonas putida genome using a combinatorial deletion method based on minitransposon insertion and the Flp-FRT recombination system. Methods Mol Biol. 813:249-66. [PubMed:22083747]
de Las Heras A, Fraile S, de Lorenzo V (2012) Increasing signal specificity of the TOL network of Pseudomonas putida mt-2 by rewiring the connectivity of the master regulator XylR. PLoS Genet. 8(10):e1002963. [PubMed:23071444] [PubMed Central:PMC3469447]
Benedetti IM, de Lorenzo V, Silva-Rocha R (2012) Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system. PLoS One. 7(12):e52000. [PubMed:23284849] [PubMed Central:PMC3532404]
Silva-Rocha R, de Lorenzo V (2012)A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria. PLoS One. 7(4):e34675. [PubMed:22493710] [PubMed Central:PMC3321037]
Herman D, Ochoa D, Juan D, Lopez D, Valencia A, Pazos F (2011) Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinformatics. 12:363. [PubMed:21910884] [HTML] [PDF] [Mirrortree and related programs] [Mirrortree web server]
Kumar A, Redondo-Muñoz J, Perez-Garcia V, Cortes I, Chagoyen M, Carrera AC (2011) Nuclear but not cytosolic phosphoinositide 3-kinase beta has an essential function in cell survival. Mol Cell Biol. 31(10):2122-2133. [PubMed:21383062] [HTML] [PDF]
Tamames JA, Ramos MJ (2011) Metals in proteins: cluster analysis studies. J Mol Model. 17(3):429-42. [PubMed:20490881]
Silva-Rocha R, de Jong H, Tamames J, de Lorenzo V (2011) The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Syst Biol. 11;5:191. [PubMed:22078029] [PubMed Central:PMC3253710]
Silva-Rocha R, de Lorenzo V (2011) A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations. Mol Biosyst. 7(11):2982-90. [PubMed:21853168]
Valls M, Silva-Rocha R, Cases I, Muñoz A, de Lorenzo V (2011) Functional analysis of the integration host factor site of the σ(54) Pu promoter of Pseudomonas putida by in vivo UV imprinting. Mol Microbiol. 82(3):591-601. [PubMed:21958188]
Martínez-García E, de Lorenzo V (2011) Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol. 13(10):2702-16. [PubMed:21883790]
de Las Heras A, Chavarría M, de Lorenzo V (2011) Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation. Mol Microbiol. 82(2):287-99. [PubMed:21923773]
Silva-Rocha R, de Lorenzo V (2011) Implementing an OR-NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli. Mol Biosyst. 7(8):2389-96. [PubMed:21584342]
Porcar M, Danchin A, de Lorenzo V, Dos Santos VA, Krasnogor N, Rasmussen S, Moya A (2011) The ten grand challenges of synthetic life. Syst Synth Biol. 5(1-2):1-9. [PubMed:21949672] [PubMed Central:PMC3159694]
de las Heras A, de Lorenzo V (2011) In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Anal Bioanal Chem. 400(4):1093-104. [PubMed:21174197]
Zafra O, Fraile S, Gutiérrez C, Haro A, Páez-Espino AD, Jiménez JI, de Lorenzo V (2011) Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins. Environ Microbiol. 13(4):960-74. [PubMed:21219561]
Chavarría M, Santiago C, Platero R, Krell T, Casasnovas JM, de Lorenzo V (2011) Fructose 1-phosphate is the preferred effector of the metabolic regulator Cra of Pseudomonas putida. J Biol Chem. 286(11):9351-9. [PubMed:21239488] [PubMed Central:PMC3058975]
de Lorenzo V (2011) Beware of metaphors: chasses and orthogonality in synthetic biology. Bioeng Bugs. 2(1):3-7. [PubMed:21636982]
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 (2011) The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol. 13(9):2389-402. [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
