· 1995. M.Sc. Biochemistry.
Universidad Autonoma de Madrid.
· 2001. Ph.D.
Sciences (Bioinformatics). Universidad
Autónoma de Madrid. Thesis: “Protein
Interactions. Computational Techniques”.
· 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).
Spanish,
Galician, English, German (learning).
· 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, Python, 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.
· 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).
· 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.
· International Workshop “New Vistas in
Computational Systems and Synthetic Biology”. Vigo
(Spain), May 2019.
· 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. 2015-2020.
· 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 (2013-2020).
· Jury in more than 20 PhD thesis in national
and international universities.
· “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. (2017-2020).
· SAF2016-78041-C2-2-R. “Identification of
modules associated to phato-phenotypes in molecular
networks.” (2016-2019).
· PID2019-108096RB-C22. “Network-based
approaches for assisting in the diagnosis of rare diseases based on
genotype-phenotype associations”. (2020-2023)
· Evaluating the impact on/by gastro-intestinal
(GI) tract microbiomes (human and domestic animal) in assessments under EFSA’s
remit. European Food Safety Authority (EFSA) (GP/EFSA/ENCO/2020/02 - Thematic
grants: Preparedness for future challenges in specific areas of EFSA`s work). (2021-2023)
Overview (JCR)
· 89 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, ....
· 4,030 citations excluding self-citations (WoS).
·
h-index:
33. (WoS).
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*, Adrian Garcia-Moreno & Juan C. Oliveros. (2018). Automatic detection of
genomic regions with informative epigenetic patterns. BMC Genomics. 19:847.
· Javier López-Ibáñez, Laura T Martín, Mónica Chagoyen
& Florencio Pazos. (2019).
Bacterial Feature Finder (BaFF) - a system for
extracting features overrepresented in sets of prokaryotic organisms. Bioinformatics.
35(18):3482-3483.
· Rafael Torres-Perez, Juan A. Garcia-Martin, Lluis Montoliu, Juan C. Oliveros*
and Florencio Pazos*. (2019).
WeReview: CRISPR Tools - Live Repository of Computational
Tools for Assisting CRISPR/Cas Experiments. Bioengineering. 6:63.
·
Monica Chagoyen, Juan A G Ranea and Florencio
Pazos. (2019).
Applications of molecular networks in biomedicine. Biology Methods and Protocols. 4(1):bpz012.
· Florencio Pazos*
& Mónica Chagoyen.
(2019). Characteristics and evolution of the ecosystem of software tools
supporting research in molecular biology. Brief Bioinform.
20(4):1329-1336.
· Fernando M. Jabato,
Pedro Seoane, James R. Perkins,
Elena Rojano, Adrián García Moreno, Mónica Chagoyen,
Florencio Pazos, Juan A. G. Ranea. (2020). Systematic identification of genetic systems associated with
phenotypes in patients with rare genomic copy number variations. Human
Genetics. doi: 10.1007/s00439-020-02214-7.
· Elena
Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane,
Florencio Pazos, James R. Perkins, Juan A. G. Ranea. (2020). Phenotype-genotype
comorbidity analysis of patients with rare disorders provides insight into
their pathological and molecular bases. PLoS Genetics 16(10):e1009054.
·
Borja Pitarch,
Juan A. G. Ranea, Florencio Pazos. (2020). Protein Residues Determining Interaction Specificity In Paralogous Families. Bioinformatics doi: 10.1093/bioinformatics/btaa934.
· Juan Antonio Garcia-Martin, Max Chavarria, Victor de Lorenzo,
Florencio Pazos. (2020).
Concomitant prediction of environmental fate and toxicity of chemical
compounds. Biology Methods and Protocols 5(1):bpaa025.
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.
· Florencio Pazos*,
Mónica Chagoyen. (2020). "Network
Analysis in Systems Biology". In Comprehensive Foodomics.
pp. 434-445. Alejandro Cifuentes (Ed.)
Elsevier.
· F. M.
Jabato, Pedro Seoane, James R. Perkins,
Elena Rojano, Adrián García Moreno, M. Chagoyen,
Florencio Pazos & Juan A. G. Ranea. (2020). Systematic identification of genetic
systems associated with phenotypes in patients with rare genomic copy number
variations. Hum Genet.
https://doi.org/10.1007/s00439-020-02214-7
Books/Monographs:
· Florencio Pazos & Mónica Chagoyen. (2015). Practical Protein Bioinformatics. Springer.
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, Cardiovascular
Res., 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., Biology
Methods and Protocols (BIOMAP), Advances in Bioinformatics, Biomed Res. Intntl., Insight Knowledge, Dataset Papers in Biology.
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)
· Project evaluator for Sadooq Al Watan (UAE)
· Grant evaluator for Research
Foundation Flanders (FWO)
· Grant evaluator for Deutsche Forschungsgemeinschaft (German Research Foundation)
· Project evaluator for "COV20 - Proyectos de investigación sobre el virus
SARS-CoV-2 y la enfermedad CoVid-19, Convocatoria 2020" (ISCIII)
·
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
@fpazos_bioinf
http://csbg.cnb.csic.es