Florencio Pazos. Publications

With links to the papers, additional material, software, servers, etc.

Papers:

Florencio Pazos, Osvaldo Olmea and Alfonso Valencia (1997). A graphical interface for correlated mutations and other structure prediction methods. CABIOS. 13(3):319-321.
[PubMed:9183539] [HTML] [PDF] [PlotCorr software]
Florencio Pazos, Manuela Helmer Citterich, Gabriele Ausiello and Alfonso Valencia (1997). Correlated Mutations Contain Information About Protein-Protein Interaction. Journal of Molecular Biology. 271(4):511-523.
[PubMed:9281423] [HTML] [PDF]
Florencio Pazos, Burkhard Rost and Alfonso Valencia (1999). A platform for integrating threading results with other information. Bioinformatics. 15(12):1062-1063.
[PubMed:10745999] [HTML] [PDF] [Threadlize software]
Florencio Pazos, Pedro Heredia, Alfonso Valencia & Javier de las Rivas (2001). Threading Structural Model of the Manganese-Stabilizing Protein PsbO Reveals Presence of Two Possible beta-Sandwich Domains. Proteins: Structure, Funcion and Genetics. 45(4):372-381.
[PubMed:11746685] [HTML] [PDF] [PsbO model]
Florencio Pazos & Alfonso Valencia (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering. 14(9):609-614.
[PubMed:11707606] [HTML] [PDF] [MirrorTree program] [Multiple sequence alignments for E coli proteins]
Volker A. Eyrich, Marc A. Mart-Renom, Dariusz Przybylski, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali & Burkhard Rost (2001). EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 17(12):1242-1243.
[PubMed:11751240] [HTML] [PDF] [EVA main site] [EVA spanish mirror]
Daniel Fischer, Arne Elofsson, Leszek Rychlewski, Florencio Pazos, Alfonso Valencia, Burkhard Rost, Angel R. Ortiz, Roland L. Dunbrack Jr. (2001). CAFASP2: The second critical assessment of fully automated structure prediction methods. Proteins: Structure, Function and Genetics 45(S5): 171-183.
[PubMed:11835495] [HTML] [PDF] [CAFASP2 web site] [Contact prediction server]
Florencio Pazos & Alfonso Valencia (2002). In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins: Structure, Function and Genetics 47(2): 219-227.
[PubMed:11933068] [HTML] [PDF] [E coli database of predicted interactions]
Piero Fariselli, Florencio Pazos, Alfonso Valencia & Rita Casadio (2002). Prediction of protein-protein interaction sites in heterocomplexes with neural networks. European Journal of Biochemistry. 269(5):1356-1361.
[PubMed:11874449] [PDF] [PS] [ISPRED server]
Alfonso Valencia & Florencio Pazos (2002). Computational methods for the prediction of protein interactions. Current Opinion in Structural Biology. 12(3):368-373.
[PubMed:12127457] [HTML] [PDF]
David de Juan, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Piero Fariselli & Rita Casadio. (2003). A neural network approach to evaluate fold recognition results. Proteins: Structure, Function and Genetics. 50(4):600-608.
[PubMed:12577266] [HTML] [PDF] [LIBELLULA server]
Antonio del Sol, Florencio Pazos & Alfonso Valencia. (2003). Automatic Methods for Predicting Functionally Important Residues. Journal of Molecular Biology. 326(4):1289-1302.
[PubMed:12589769] [HTML] [PDF] [MTreedet program] [Treedet web server]
Alfonso Valencia & Florencio Pazos. (2003). Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal. 44:411-426.
[PubMed:12647397] [Book web site]
Antonio Maraver, Ana Oña, Fernando Abaitua, Dolores Gonzalez, Roberto Clemente, Jose A. Ruiz-Diaz, Jose R. Caston, Florencio Pazos & Jose F. Rodriguez. (2003). The Oligomerization Domain of VP3, the Scaffolding Protein of Infectious Bursal Disease Virus, Plays a Critical Role in Capsid Assembly. Journal of Virology. 77(11):6438-6449.
[PubMed:12743301] [HTML] [PDF]
Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Marti-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali & Burkhard Rost. (2003). EVA: evaluation of protein structure prediction servers. Nucleic Acids Research. 31(13):3311-3315.
[PubMed:12824315] [HTML] [PDF] [EVA main site] [EVA spanish mirror]
Monica Balsera, Juan Arellano, Florencio Pazos, Damian Devos, Alfonso Valencia & Javier De Las Rivas. (2003). A single-tryptophan embedded in a four alpha-helices bundle domain of PsbQ protein. Eur J Biochem. 270(19):3916-3927.
[PubMed:14511373] [HTML] [PDF]
Florencio Pazos, Alfonso Valencia & Victor De Lorenzo. (2003). The organization of the Microbial Biodegradation Network from a Systems-Biology perspective. EMBO Rep. 4(10):994-999.
[PubMed:12973298] [HTML] [PDF] [Representations of the network and additional data]
Volker A. Eyrich, Dariusz Przybylski, Ingrid Y. Koh, Osvaldo Grana, Florencio Pazos, Alfonso Valencia & Burkhard Rost. (2003). CAFASP3 in the spotlight of EVA. Proteins. 53(S6): 548-560.
[PubMed:14579345] [HTML] [PDF] [EVA main site] [EVA spanish mirror]
Florencio Pazos & Michael J. E. Sternberg. (2004). Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci USA. 101(41):14754-14759.
[PubMed:15456910] [HTML] [PDF]
Florencio Pazos, David Guijas, Alfonso Valencia & Victor De Lorenzo. (2005). MetaRouter: bioinformatics for bioremediation. Nucleic Acids Research. 33:D588-D592.
[PubMed:15608267] [HTML] [PDF] [MetaRouter server] [Additional information]
Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost & Alfonso Valencia. (2005). EVAcon: a protein contact prediction evaluation service. Nucleic Acids Research. 33:W347-W351.
[PubMed:15980486] [HTML] [PDF] [EVA main site] [EVAcon]
Florencio Pazos, Juan A. G. Ranea, David Juan & Michael J. E. Sternberg. (2005). Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. Journal of Molecular Biology. 352(4):1002-1015.
[PubMed:16139301] [HTML] [PDF] [online additional material] [MirrorTree/tol-mirrortree programs]
Florencio Pazos & Jung-Wook Bang. (2006). Computational Prediction of Functionally Important Regions in Proteins. Current Bioinformatics. 1(1):15-23.
[HTML] [PDF]
Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJ. (2006). The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci. 361(1467):441-451.
[PubMed:16524832] [HTML]
Florencio Pazos, Antonio Rausell & Alfonso Valencia. (2006). Phylogeny-independent detection of functional residues. Bioinformatics. 22(12):1440-1448.
[PubMed:16551661] [HTML] [PDF] [Supplementary information] [MTreedet/Xdet programs]
Jose M. G. Izarzugaza, David Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia & Florencio Pazos. (2006). TSEMA: Interactive Prediction of Protein Pairings Between Interacting Families. Nucleic Acids Research. 34:W315-W319.
[PubMed:16845017] [HTML] [PDF] [TSEMA web server @CNIO]
Angel Carro, Michael Tress, David Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia & Ana Rojas (2006). TreeDet: A Web Server to Explore the Sequence Space. Nucleic Acids Research. 34:W110-W115.
[PubMed:16844971] [HTML] [PDF] [TreeDet web server]
Gómez, MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A. (2007). The environmental fate of organic pollutants through the global microbial metabolism. Mol Syst Biol. 3:114.
[PubMed:17551509] [HTML] [PDF] [BDPserver]
David Juan, Florencio Pazos & Alfonso Valencia. (2008). High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA. 105(3):934-939.
[PubMed:18199838] [HTML] [PDF] [ECID system]
Jung-Wook Bang, Derek J. Crockford, Elaine Holmes, Florencio Pazos, Michael J. E. Sternberg, Stephen H. Muggleton, Jeremy K. Nicholson. (2008). Integrative Top-Down System Metabolic Modeling in Experimental Disease States via Data-Driven Bayesian Methods. J Proteome Res. 7(2):497-503.
[PubMed:18179164] [HTML] [PDF]

Jose M. G. Izarzugaza, David Juan, Carles Pons, Florencio Pazos*, Alfonso Valencia. (2008). Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics. 9:35.
[PubMed:18215279] [HTML] [PDF] [TAG-TSEMA web server @CNIO]

Angela del Pozo, Florencio Pazos, Alfonso Valencia. (2008). Defining functional distances over gene ontology. BMC Bioinformatics. 9:50.
[PubMed:18221506] [HTML] [PDF]

David Juan, Florencio Pazos, Alfonso Valencia. (2008). Co-evolution and co-adaptation in protein networks. FEBS Lett. 582(8):1225-1230.
[PubMed:18282476] [HTML] [PDF]

Florencio Pazos*, David Juan, Jose M Izarzugaza, Eduardo Leon, Alfonso Valencia. (2008). Prediction of protein interaction based on similarity of phylogenetic trees. Methods Mol Biol. 484:523-535.
[PubMed:18592199] [HTML] [mirrortree/tol-mirrortree programs] [ECID system] [TSEMA web server]
Florencio Pazos & Alfonso Valencia. (2008). Protein co-evolution, co-adaptation and interactions. EMBO J. 27(20):2648-2655.
[PubMed:18818697] [HTML] [PDF] [mirrortree and related programs]
Daniel Lopez & Florencio Pazos*. (2009). Gene ontology functional annotations at the structural domain level. Proteins. 76(3):598-607.
[PubMed:19241468] [HTML] [PDF] [Scop2go database]
Monica Chagoyen & 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] [More information]

Antonio Rausell, David Juan, Florencio Pazos & 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]

David Ochoa & 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]

Juan C. Triviño & 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]

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. (2010). Genetic polymorphisms among C57BL/6 mouse inbred strains. Transgenic Res.
[Pubmed:20506040] [HTML] [PDF]

Monica Chagoyen & Florencio Pazos. (2011). MBRole: enrichment analysis of metabolomic data. Bioinformatics.27(5):730-731.
[Pubmed:21208985] [HTML] [PDF] [MBROLE server]

Mark N. Wass, Gloria Fuentes, Carles Pons, Florencio Pazos & Alfonso Valencia. (2011). Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol. 7:469.
[PubMed:21326236] [HTML] [PDF] [Summary]

Highlighted Book Chapters:

Florencio Pazos, Luis Sanchez, Juan A. Garcia, Miguel A. Andrade, Silvia Atrian and Alfonso Valencia (1997). "Comparative analysis of different methods for the detection of specificity regions in protein families". In Bio-Computing and Emergent Computation (BCE97). pp. 132-145. D. Lundh; B. Olson; A. Narayanan (Eds.)
[PostScript] [Book web site]
F. Abascal, R. Alonso-Allende, C. Blaschke, B. Contreras, D. Devos, J. Dopazo, J. M. Fernandez, J. A. Garcia-Ranea, M. Gonzalez, J. Herrero, J. C. Oliveros, O. Olmea, F. Pazos, R. Roca, L. Sanchez-Pulido, A. Del Sol, J. Tamames, A. Valencia. (2001). "Bioinformatics for Functional and Structural Genomics at the Protein Design Group CNB-CSIC". In Protein Sequence Analysis In The Post-Genomic Era. pp. 149-165. Eds. Rita Casadio, Lanfranco Masotti - Bologna CLUEB.
[Book web site] [ on-line supplementary material ]
Devos D., Pazos F., Olmea O., de Juan D., Grana O, Fernandez J.M. and Valencia A. (2002). "The role of sequence information in protein structure prediction". In Protein Structure Prediction: Bioinformatic Approach pp. 127-142. Ed. Tsigelny, I. International University Line publishers.
[Book web site]
Devos D., Merino E., Pazos F. and Valencia A. (2002) “Multiple sequence alignments information in structure and function prediction”. In Artificial Intelligence and Heuristic Methods for Bioinformatics. pp. 83-94. IOS Press publishers.
[Book web site]
Tamaddoni-Nezhad, A., Kakas, A., Muggleton, S. & Pazos, F. (2004). "Modelling inhibition in metabolic pathways through Abduction and Induction". In Rui Camacho, Ross D. King, Ashwin Sirinivasan (Eds.) Inductive Logic Programming, 14th International Conference, ILP 2004, Proceedings. Lecture Notes in Computer Science. vol. 3194/2004. pp. 305-322. Springer-Verlag, Heidelberg.
[PDF] [Publication web site]
Florencio Pazos, David Guijas, Manuel J. Gomez, Almudena Trigo, Victor de Lorenzo & Alfonso Valencia. (2005). "The Biodegradation Network, a New Scenario for Computational Systems Biology". In Computational Methods in Systems Biology: Subseries of Lecture Notes in Bioinformatics. V. Danos, V. Schachter (Eds). vol. 3082/2005. pp. 252-256. Springer-Verlag GmbH, Heidelberg.
[Book web site]
Manuel Gomez, Ramon Alonso-Allende, Florencio Pazos, Osvaldo Grana, David Juan & Alfonso Valencia. (2005). "Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories". In Transactions on Computational Systems Biology I: Subseries of Lecture Notes in Computer Science. Corrado Priami (Ed). vol. 3380/2005. pp. 1-13. Springer-Verlag GmbH, Heidelberg.
[Book web site]
Valencia, A., Pazos, F. (2008). "Computational Methods to predict protein interaction partners". In Protein-protein interactions and networks. pp. 67-81. Ed. Panchenko, A. R. & Przytycka, T.M. Springer-Verlag , London.
[Book web site]
Valencia, A., Pazos, F. (2009). "Prediction of protein-protein interactions from evolutionary information". In Structural Bioinformatics, 2nd edition. pp. 615-632. Ed. Gu, J. & Bourne, P.E. John Wiley & Sons, New Jersey.
[Book web site]
Pazos, F., Valencia, A. (2010). "Protein interactions from an evolutionary perspective". In Statistical and Evolutionary A\ nalysis of Biological Networks. pp. 127-143 Eds. Stumpf, M.P.H. & Wiuf, C. Imperial College Press, London.
[Book web site]

[F. Pazos' Curriculum Vitae] [Computational Systems Biology Group Publications]

Dr. Florencio Pazos Cabaleiro.
Computational Systems Biology Group
Centro Nacional de Biotecnologia (C.N.B. - C.S.I.C.)
C/ Darwin, 3. Campus UAM. Cantoblanco. 28049 Madrid.
Tlf: +34-91-5854669. Fax: +34-91-5854506.
e-mail: