Last update: July 2018

 

Florencio Pazos Cabaleiro

Curriculum Vitae

 

Degrees

· 1995. M.Sc. Biochemistry. Universidad Autonoma de Madrid.

· 2001. Ph.D. Sciences (Bioinformatics). Universidad Autónoma de Madrid. Thesis: “Protein Interactions. Computational Techniques”.

Research & Professional Activities

· 1994: Experimental work as student collaborator with the group of Dr. Rafael Manso. Project: "Molecular Adaptation of the Animal Muscle to Training". Centro de Biología Molecular Severo Ochoa (CBMSO, UAM.-CSIC).

·1995-2001: Bioinformatics. PhD student with Dr. Alfonso Valencia. Protein Design Group (CNB-CSIC). Main project: "Development of New Methods for Predicting Protein Structure and Protein-protein Interactions from Evolutionary Information”.

· 1999-2001: Consulting for Lion Biosciences AG. Heidelberg.

· 2001-2002: Senior Scientist/Project Leader. ALMA Bioinformatics, SL. Madrid. Main projects: Organization and teaching in the bioinformatics courses; bioinformatics for biodegradation.

· 2003-2005: Research Associate. Imperial College London (London). Prof. Michael Sternberg’s Structural Bioinformatics Group. Main projects: Modeling of metabolic networks; protein function prediction.

· Feb. 2005 – Jun. 2006: Recipient of a “Ramón y Cajal” Contract from the Spanish Ministry for Education and Science.

· Since Jun. 2006: Tenured Scientist (“Científico Titular”) of the Spanish Research Council (CSIC). Currently Group Leader of the Computational Systems Biology Group at the National Center for Biotechnology (CNB-CSIC).

Languages

Spanish, Galician, English, German (learning).

Computer Expertise

· Operative systems and working environments: MS-DOS, MS-Windows, UNIX (SGI-IRIX, Sun-Solaris, Linux and others), XWindow, Mac OS 9.x/X, VAX-VMS.

· Programming languages: C, C++, Perl, QBasic, VisualBasic, [PostScript], Java (learning), [SQL]. Under operative systems and working environments: MS-DOS, MS-Windows, UNIX, XWindow. Programming for multiprocessor machines and clusters. Programming of graphical interfaces for MS-Windows and XWindow.

· Internet: HTML, CGIs, Javascript (learning), TCP/IP programming.

· System Administration of Unix Systems.

· Bioinformatics: Knowledge of the main bioinformatics packages, databases and other bioinformatics resources.

Highlighted Courses

· Perl course of the Spanish Bioinformatics Network (Granada, 1997).

· Course "Advanced System Administration". Silicon Graphics (Madrid, 1997).

· FEBS course: "Frontiers of Protein Structure Prediction". IRBM (Rome, 1997).

· Second Bologna Summer School on Biotechnology (BOSS'99) (Bologna, 1999).

· Various courses of the Imperial College Staff Development Program: German, Writing research for publication, Project management, Preparing grant applications, ... (London, 2003-2004).

Highlighted Invited Talks

· FEBS Congress: "Young Scientists' View on Molecular Biology". Goslar, Germany, 1998.

· XIII Meeting of the Spanish Society for Biochemistry and Molecular Biology (SEBBM). Granada,  2000

· II y III Meetings of the Spanish Bioinformatics Network. Malaga (2001) and Salamanca (2002).

· “Bioinformatics for Biodegradation”. University College London. Nov. 2003.

· Inaugural lectura of the “Bioinformatics Course”. Escuela Superior de Tecnología y Gestión de Bragança. Portugal, Apr. 2005.

· GTCbio’s “Protein Discovery and Development Meeting”. Washington DC, USA, Sep. 2007.

· XXXI Meeting of the Spanish Society for Biochemistry and Molecular Biology (SEBBM). Bilbao, Sep. 2008.

· GIAPP’09. “Artificial intelligence methods applied to protein holding”. Puebla, Mexico, Apr. 2009.

· Bioinformatics Course. Pontificia Universidad Católica de Chile. Santiago de Chile, Sep. 2009.

· V Meeting of the Spanish Systems Biology Network. Madrid, Dic. 2009.

· Avanced seminar on –omics technologies. Spanish Biotechnology Society (SEBiot). Pamplona. Sep. 2010.

· “Reality and Prospects of Synthetic Biology”. Round table of the “Fundación Alternativas”. Madrid. Oct. 2010.

· New Trends in Proteomics. 4th Meeting of the Spanish Proteomics Society. Segovia. Feb. 2011.

· 75th Anniversary of the Mexican Polytechnic Institute. Mexico DF. Nov. 2011.

· “Root Systems Biology”. Taipei, Taiwan. September 2012.

· “El Escorial” UCM Sumer courses. El Escorial. Madrid. July 2013.

· Meeting of the American Institute of Mathematical Sciences. Madrid. July 2014.

· Biotechnology Week UPM. Madrid. October 2014.

· XXXVIII Meeting of the SEBBM. Valencia, September, 2015.

· Instituto de Química-Física Rocasolano (CSIC). Madrid, January 2016.

· Instituto de Ecología de Xalapa. Veracruz, México. July 2016.

· Colloquium on Multilevel Biological Design. CNB. Madrid. January 2017.

· Jornadas de Biotecnologia UPM. Madrid. February 2017.

· Instituto de Investigaciones Marinas. Vigo. February 2017.

· EMBO Workshop Integrating genomics and biophysics to comprehend functional genetic variation. Turin (Italy), September 2017.

· Mini Symposium on Structural Bioinformatics in memoriam Angel Ramirez Ortiz. CBMSO. Madrid, May 2018.

· Institut Imagine. Paris (France), June 2018.

Teaching activities

· 1994-1998: Teaching in various university courses: MS-DOS, C Programming, Linux, MS-Word, etc. “Aulas de Informática” (AdI-UAM, Madrid).

· 1997 and 1998: "Molecular design. Computational protein structure prediction and modelling" (Universidad Complutense/Comunidad de Madrid).

· Oct. 2000: Session in the "Inter-Universitary DEA/DES Master in Bioinformatics" (FUNDP, Belgium).

· Nov. 2001: “Bioinformática. Programa de Doctorado de Calidad en Biotecnología. (Dep. Microbiología. Universidad de León).

· Nov. 2001 and Jul. 2002: "Specialist in Bioinformatics" (Universidad Complutense, Madrid).

· 1999-2001, 2005-2011: Collaboration in various PhD courses (Bioinformatics, Structure of Macromolecules, Microbial Biotechnology). Departamento de Biología Molecular, Universidad Autónoma de Madrid.

· Mar. 2002 and Jan. 2003: Organization and teaching in the I and II “Theoretical and practical course on bioinformatics”. ALMA Bioinformatics, S.L. Madrid.

· Apr. 2005: Inaugural Lecture of the “Bioinformatics Course”. Escuela Superior de Tecnología y Gestión de Bragança. Bragança, Portugal.

· May. 2005: Session in the “Bioinformatics for Health Sciences” Master. Universidad Ponpeu-Fabra / Universidad de Barcelona.

· Jun. 2005: Session in the “Master en Bioinformática 2005”. Universidad Complutense de Madrid.

· 2005, 2006, 2007 & 2008. Sessions in the “Summer Course on Bioinformatics”. Universidad Complutense. Madrid.

· Jun. 2006. Organization and teaching of a 2-weeks module on “Sequence Analysis” for the “TecBio Master”. Consorzio-21. Sardinia, Italy.

· Jul. 2007: Organization and teaching in the Bioinformatics activity for the 2007 round of the “Spain-Portugal Summer Stays” (ESCIVE, FECYT).  Madrid.

· Basic course on “Managing, visualizing and predicting protein structure” for CNB staff. Madrid 2007-2008

· Organization and teaching in the 2-week module on “Biological Networks and Systems Biology” for the “Master en Bioinformática”. 2006-2012:Universidad Complutense de Madrid; 2013-2017: Escuela de Sanidad, I. Salud Carlos III Madrid.

· Apr. 2008: Organization and teaching in the 2-week PhD course “Biological Networks and Systems Biology”. Universidad Autónoma de Madrid.

· Collaboration in the subject “Bioinformatics and Data Management”. University of Malaga. 2015-2017.

· Collaboration in various Master courses of the U. Autónoma Madrid: Bacterial Biotechnology, Understanding Biomolecules, …

· Collaboration in various degree and master courses. Universidad Carlos III Madrid (2013-2017).

· Jury in more than 20 PhD thesis in national and international universities.

Awarded Projects

· “Ramón Y Cajal” project: “Modeling the dynamical behavior of the proteome combining protein interaction networks with expression data”. 2005. Spanish Ministry for Education and Science.

· BIO-2006-15318. “Functional Study of Protein Interaction Networks”. (2007-2009). Spanish Ministry for Education and Science.

· PIE 200620I240. “Functional Study of Biological Networks”. (2007). Spanish Ministry for Education and Science.

· BIO-2009-11966. “Functional Study of Protein Interaction Networks”. (2010). Spanish Ministry for Science and Innovation.

· BIO-2010-22109. “Functional Study of Protein Interaction Networks”. (2011-2013). Spanish Ministry for Economy and Competitiveness.

· BIO2015-72091-EXP. “Chemical Profiles: a new methodology to capture relationships between structures of chemical compounds and biological processes”. PI Monica Chagoyen. (2015-2017).

· SAF2016-78041-C2-2-R. “Identification of modules associated to phato-phenotypes in molecular networks.” (2016-2019).

Publications

Overview (ISI-WOK data)

83 articles in peer-reviewed international journals since 1997. Including Nature Review Genetics, Nature Chemical Biology, Proc Natl Acad Sci USA, Curr Opin Str Biol, J Mol Biol, Mol Syst Biol, Acta Cryst. D., EMBO J, Nucl Acids Res, Bioinformatics, ....

2984 citations excluding self-citations;
h-index: 26.

Journal Articles (PubMed)

· Florencio Pazos, Osvaldo Olmea and Alfonso Valencia (1997). A graphical interface for correlated mutations and other structure prediction methods. Comp App Biol Sci 13(3):319-321.

· Florencio Pazos, Manuela Helmer Citterich, Gabriele Ausiello and Alfonso Valencia (1997). Correlated Mutations Contain Information About Protein-Protein Interaction. J Mol Biol. 271(4):511-523.

· Florencio Pazos, Burkhard Rost and Alfonso Valencia (1999). A platform for integrating threading results with protein family analysis. Bioinformatics. 15(12):1062-1063.

· 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. 45(4):372-381.

· Florencio Pazos & Alfonso Valencia (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14(9):609-614.

· Volker A. Eyrich, Marc A. Mart-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, 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.

· 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. 45(S5): 171-183.

· Florencio Pazos & Alfonso Valencia (2002). In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins. 47(2): 219-227.

· Piero Fariselli, Florencio Pazos, Alfonso Valencia & Rita Casadio (2002). Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem. 269(5): 1356-1361.

· Alfonso Valencia & Florencio Pazos (2002). Computational Methods for the Prediction of Protein Interactions. Curr Op Str Biol.  12(3): 368-373.

· David de Juan, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Piero Fariselli & Rita Casadio. (2003). A neural network approach to evaluate fold recognition results. Proteins. 50(4):600-608.

· Antonio del Sol, Florencio Pazos & Alfonso Valencia. (2003). Automatic Methods for Predicting Functionally Important Residues. J Mol Biol. 326(4):1289-1302.

· Alfonso Valencia, Florencio Pazos. (2003). Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal. 44:411-426.

· Antonio Maraver, Ana Oña, Fernando Abaitua, Dolores González, Roberto Clemente, Jose A. Ruiz-Díaz, Jose R. Castón, 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. J Virol. 77(11):6438-6449.

· 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.

· 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.

· 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.

· Volker A. Eyrich, Dariusz Przybylski, Ingrid Y.Y. Koh, Osvaldo Grana, Florencio Pazos, Alfonso Valencia, Burkhard Rost. (2003). CAFASP3 in the spotlight of EVA. Proteins. 53(S6):548-560.

· Florencio Pazos & Michael J. E. Sternberg. (2004). Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A. 101(41):14754-14759.

· Florencio Pazos*, David Guijas, Alfonso Valencia & Victor De Lorenzo. (2005). MetaRouter: bioinformatics for bioremediation. Nucleic Acids Research. 33:D588-D592.

· 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.

· 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.

· Florencio Pazos* & Jung-Wook Bang. (2006). Computational Prediction of Functionally Important Regions in Proteins. Current Bioinformatics. 1(1):15-23.

· 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.

· Florencio Pazos*, Antonio Rausell & Alfonso Valencia. (2006). Phylogeny-independent detection of functional residues. Bioinformatics. 22(12):1440-1448.

· José 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.

· 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.

· Manuel J. Gomez, Florencio Pazos, Francisco J. Guijarro, Victor de Lorenzo, Alfonso Valencia. (2007). The environmental fate of organic pollutants through the global microbial metabolism. Molecular Systems Biology. 3:114.

·David Juan, Florencio Pazos, Alfonso Valencia. (2008). High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci U S A. 105(3): 934-939.

· 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. Journal of Proteome Research. 7(2):497-503.

· José 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(1):35.

· Angela del Pozo, Florencio Pazos, Alfonso Valencia. (2008). Defining functional distances over Gene Ontology. BMC Bioinformatics. 9(1):50.

· David Juan, Florencio Pazos, Alfonso Valencia. (2008). Co-evolution and co-adaptation in protein networks. FEBS Lett. 582(8):1225-1230.

· 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.

· Florencio Pazos & Alfonso Valencia. (2008). Protein co-evolution, co-adaptation and interactions. EMBO J. 27(20):2648-2655.

· Daniel Lopez & Florencio Pazos*. (2009). Gene ontology functional annotations at the structural domain level. Proteins. 76(3):598-607.

· 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.

· 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.

· David Ochoa & Florencio Pazos*. (2010). Studying the co-evolution of protein families with the Mirrortree web server. Bioinformatics. 26(10):1370-1371.

· 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.

· 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.

· Monica Chagoyen & Florencio Pazos*. (2011). MBRole: enrichment analysis of metabolomic data. Bioinformatics. 27(5):730-731.

· 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.

· Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia and Florencio Pazos* (2011). Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinformatics. 12:363.

· Thilo Muth, Juan A. García-Martín, Antonio Rausell, David Juan, Alfonso Valencia and Florencio Pazos* (2012). JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics. 28(4):584-586.

· 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.

· Monica Chagoyen and Florencio Pazos (2013). Tools for the functional interpretation of metabolomic experiments. Briefings in Bioinformatics. 14(6):737-744.

· David Ochoa, Ponciano García-Gutiérrez, David Juan, Alfonso Valencia and Florencio Pazos*. (2013). Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. Molecular Biosystems. 9(1):70-76.

· Natalia Pietrosemoli, Juan A. García-Martín, Roberto Solano and Florencio Pazos* (2013). Genome-Wide Analysis of Protein Disorder in Arabidopsis thaliana: Implications for Plant Environmental Adaptation. PLoS One. 8(2):e55524.

· Daniel Lopez and Florencio Pazos* (2013). Concomitant prediction of function and fold at the domain level with GO-based profiles. BMC Bioinformatics. 14(S3):S12.

· David Juan, Florencio Pazos and Alfonso Valencia (2013). Emerging methods in protein co-evolution. Nature Reviews Genetics. 14(4):249-261.

· Daniel Lopez and Florencio Pazos* (2013). COPRED: prediction of fold, GO molecular function and functional residues at the domain level. Bioinformatics. 29(14):1811-1812.

· Florencio Pazos*, Natalia Pietrosemoli, Juan A. García-Martín and Roberto Solano. (2013). Protein intrinsic disorder in plants. Frontiers in Plant Science. 4:363.

· A. Espaillat, C. Carrasco-Lopez, N. Bernardo-Garcia, N. Pietrosemoli, L. H. Otero, L. Alvarez, M. A. de Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso and F. Cava. (2014). Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Cryst D. D70:79-90.

· Mónica Chagoyen, José L. Carrascosa, Florencio Pazos* and José M. Valpuesta*. (2014). Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex. Proteins: Structure, Function, and Bioinformatics. 82(5):703-707.

· David Ochoa and Florencio Pazos. (2014). Practical aspects of protein co-evolution. Frontiers in Cell and Developmental Biology. 2:14.

· Isabel Monte, Mats Hamberg, Andrea Chini, Selena Gimenez-Ibanez, Gloria Garcia-Casado, Andrea Porzel, Florencio Pazos, Marta Boter and Roberto Solano (2014). Rational design of a ligand-based antagonist of jasmonate perception. Nature Chemical Biology. 10(8):671-676.

· David Ochoa, David Juan, Valencia, A. and Florencio Pazos (2015). Detection of significant protein co-evolution. Bioinformatics. 31(13):2166-2173

· Daniel López and Florencio Pazos (2015). Protein functional features are reflected in the patterns of mRNA translation speed. BMC Genomics. 16:513

· Mónica Chagoyen, Juan A. García-Martín and Florencio Pazos (2016). Practical analysis of specificity-determining residues in protein families. Briefings in Bioinformatics 17(2):255-261.

· Mónica Chagoyen, Javier López-Ibáñez, Florencio Pazos (2016). Functional Analysis of Metabolomics Data. Methods Mol Biol. 1415:399-406.

· Monica Chagoyen and Florencio Pazos (2016). Characterization of clinical signs in the human interactome. Bioinformatics. 32(12):1761-1765.

· Sara Fernandez-Novo, Florencio Pazos and Monica Chagoyen (2016). Rare disease relations through common genes and protein interactions. Mol Cell Probes. 30(3):178-181

· Javier López-Ibáñez, Florencio Pazos and Mónica Chagoyen (2016). MBROLE 2.0-functional enrichment of chemical compounds. Nucleic Acids Res. 44:W201-W204

· Oliveros JC, Franch M, Tabas-Madrid D, San-León D, Montoliu L, Cubas P, Pazos F. (2016). Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res. 44:W267-W271.

· Adán Alpízar, Fabio Marino, Antonio Ramos-Fernández, Manuel Lombardía, Anita Jeko, Florencio Pazos, Alberto Paradela, César Santiago, Albert J. R. Heck and Miguel Marcilla. (2017). A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens. Molecular & Cellular Proteomics 16:181-193.

· Sara González-Pérez, Florencio Pazos & Mónica Chagoyen. (2017). Factors affecting interactome-based prediction of human genes associated with clinical signs. BMC Bioinformatics. 18(1):340.

· Diego Garrido-Martín & Florencio Pazos. (2018). Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. BMC Bioinformatics. 19(1):67.

· Florencio Pazos* & Mónica Chagoyen. (2018). Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology. Brief Bioinform. doi: 10.1093/bib/bby001. [Epub ahead of print]

 

Other Articles (ISI-WOK)

· Alireza Tamaddoni-Nezhad, Antonis C. Kakas, Stephen Muggleton & Florencio Pazos. (2004). “Modelling Inhibition in Metabolic Pathways Through Abduction and Induction”. In Rui Camacho, Ross D. King, Ashwin Srinivasan (Eds.) Inductive Logic Programming, 14th International Conference, ILP 2004, Proceedings. Lecture Notes in Computer Science. vol. 3194/2004. pp. 305-322. Springer-Verlag, Heidelberg.

· Florencio Pazos, David Guijas, Manuel J. Gómez, 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.

· 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.

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 D. Lundh; B. Olson; A. Narayanan (Eds.) Bio-Computing and Emergent Computation (BCE97).pp. 132-145

· 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 Rita Casadio, Lanfranco Masotti - Bologna CLUEB. Protein Sequence Analysis In The Post-Genomic Era. pp. 149-165.

· Devos D., Pazos F., Olmea O., de Juan D., Graña 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..

· 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.

· 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.

· 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.

· Pazos, F., Valencia, A. (2010). "Protein interactions from an evolutionary perspective". In Statistical and Evolutionary Analysis of Biological Networks. pp. 127-143 Eds. Stumpf, M.P.H. & Wiuf, C. Imperial College Press, London.

·  Florencio Pazos* and Luis Sanchez-Pulido.  (2014). Protein superfamilies. Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0025587.

·  Florencio Pazos, Victor de Lorenzo. (2016). "Biodegradation Prediction Tools". In Hydrocarbon and Lipid Microbiology Protocols - Statistics, Data Analysis, Bioinformatics and Modelling. pp. 115-124. McGenity, Terry J., Timmis, Kenneth N., Nogales, Balbina (Eds.) Springer-Verlag, Berlin, Heidelberg.

·  Florencio Pazos, David de Juan. (2016). "Predicting Protein Interactions". In Hydrocarbon and Lipid Microbiology Protocols - Statistics, Data Analysis, Bioinformatics and Modelling. pp. 125-134. McGenity, Terry J., Timmis, Kenneth N., Nogales, Balbina (Eds.) Springer-Verlag, Berlin, Heidelberg.

Books/Monographs:

· Florencio Pazos & Mónica Chagoyen. (2015). Practical Protein Bioinformatics. Springer.

 

Other merits       

Referee for international journals and highlighted congresses:

Bioinformatics, Proc. Natl. Acad. Sci. USA., Journal of Molecular Biology, Proteins, Nucleic Acids Research, Trends in Biotechnology, Scientific Reports, Nature Comm., PloS ONE, Molecular Biology & Evolution, FEBS Letters, FEBS Journal, PloS Computational Biology, Briefings Bioinform., Human Genetics, Protein Science, Environmental Microbiology, Gene, Oncotargets, BMC Bioinformatics, BMC Evolutionary Biology, BMC Syst. Biol. BMC Str Biol, BMC Genomics, Enc. Life Sci., ISMB’05-06-07-08-09-10-11-13, JCAMD, Pacific Symposium in Biocomputing 08, Drug Discovery Today, JCST, JRSI, Journal of Biotechnology, Biophysical Chemistry, Transactions on Computational Biology and Bioinformatics, EURASIP Journal on Bioinformatics and Systems Biology, Automated Experimentation, Database, African J. Biotech, CMLS, Computers in Biology and Medicine.

Editorial Board:       

BMC Bioinformatics, Frontiers Cell Dev Biol., Advances in Bioinformatics, Biomed Res. Intntl., Insight Knowledge, Dataset Papers in Biology, Biology Methods and Protocols (BIOMAP).

I+D management:    

·       Since 2009. Project evaluator of the Spanish Agency for Evaluation and Foresight (ANEP).

·       Member of the Access Committee of the Barcelona Supercomputing Center (BSC/RES).

·       Project evaluator for the Wellcome Trust.

·       Evaluator for the “Juan de la Cierva” program. Madrid. May. 2010.

·       Project evaluator for the Israel Science Foundation (ISF).

·       Project evaluator for University of Luxembourg.

·       Project evaluator for Khalifa University (Abu Dhabi)

·       Project evaluator for the Netherlands Organisation for Scientific Research.

·       Project evaluator for Innovation Fund Denmark (Dinamarca)

Organization of Congresses and Meetings:          

·       5th Meeting of the Spanish Systems Biology Network – “Fostering Systems and Synthetic Biology in Southern Europe”. Madrid. Dic. 2009.

·       1st Colloquium of the Systems and Synthetic Biology Program (CNB-CSIC). Madrid. Nov. 2010.

 

 

 

Dr. Florencio Pazos Cabaleiro.

Phone. +34.915854669 / Mob. +34.629839990 / Fax. +34.915854506
pazos@cnb.csic.es

http://csbg.cnb.csic.es