F. Pazos

发表

Emerging methods in protein co-evolution

A. Valencia, D. Juan, F. Pazos, 2013, Nature Reviews Genetics.

A. Valencia, F. Pazos, M. Helmer-Citterich, 1997, Journal of molecular biology.

Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

M. Sternberg, D. Juan, F. Pazos, 2005, Journal of molecular biology.

In silico two‐hybrid system for the selection of physically interacting protein pairs

A. Valencia, F. Pazos, 2002, Proteins.

A. Valencia, F. Pazos, Alfonso Valencia, 2001, Protein engineering.

MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format.

Karin M. Verspoor, F. Pazos, T. Dandekar, 2015, F1000Research.

Protein functional features are reflected in the patterns of mRNA translation speed

F. Pazos, Daniel Lopez, 2015, BMC Genomics.

Automated prediction of protein function and detection of functional sites from structure.

M. Sternberg, F. Pazos, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Automatic methods for predicting functionally important residues.

A. Valencia, F. Pazos, A. del Sol, 2003, Journal of molecular biology.

Computational methods for the prediction of protein interactions.

A. Valencia, F. Pazos, 2002, Current opinion in structural biology.

Prediction of protein--protein interaction sites in heterocomplexes with neural networks.

A. Valencia, F. Pazos, R. Casadio, 2002, European journal of biochemistry.

Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations

F. Pazos, J. A. Ranea, M. Chagoyen, 2020, Human Genetics.

Rare disease relations through common genes and protein interactions.

F. Pazos, M. Chagoyen, Sara Fernandez-Novo, 2016, Molecular and cellular probes.

Prediction of protein-protein interactions from evolutionary information.

Alfonso Valencia, Florencio Pazos, A. Valencia, 2003, Methods of biochemical analysis.

Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases

F. Pazos, J. A. Ranea, F. M. Jabato, 2020, PLoS genetics.

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

A. Valencia, D. Juan, F. Pazos, 2008, Proceedings of the National Academy of Sciences.

Rational design of a ligand-based antagonist of jasmonate perception.

F. Pazos, M. Hamberg, R. Solano, 2014, Nature chemical biology.

Protein interactions and ligand binding: From protein subfamilies to functional specificity

Alfonso Valencia, Florencio Pazos, Antonio Rausell, 2010, Proceedings of the National Academy of Sciences.

Co‐evolution and co‐adaptation in protein networks

Alfonso Valencia, Florencio Pazos, David Juan, 2008, FEBS letters.

Protein co-evolution, co-adaptation and interactions

Alfonso Valencia, Florencio Pazos, A. Valencia, 2008, The EMBO journal.

Emerging methods in protein co-evolution

Alfonso Valencia, Florencio Pazos, David Juan, 2013 .

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

Alfonso Valencia, Florencio Pazos, David Juan, 2013, Molecular bioSystems.

The organization of the microbial biodegradation network from a systems‐biology perspective

Alfonso Valencia, Florencio Pazos, Víctor De Lorenzo, 2003, EMBO reports.

Protein intrinsic disorder in plants

Florencio Pazos, Natalia Pietrosemoli, F. Pazos, 2013, Front. Plant Sci..

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens*

F. Pazos, A. Heck, A. Ramos-Fernández, 2016, Molecular & Cellular Proteomics.

Computational Methods to Predict Protein Interaction Partners

Alfonso Valencia, Florencio Pazos, A. Valencia, 2008, Protein-protein Interactions and Networks.

Practical Protein Bioinformatics

F. Pazos, M. Chagoyen, 2014, Springer International Publishing.

Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View

F. Pazos, M. Chagoyen, J. A. Ranea, 2022, Genes.

Concomitant prediction of environmental fate and toxicity of chemical compounds

F. Pazos, V. de Lorenzo, J. A. García-Martín, 2020, Biology methods & protocols.

Automatic detection of genomic regions with informative epigenetic patterns

F. Pazos, A. García-Moreno, J. C. Oliveros, 2018, BMC Genomics.

Sequence analysis Phylogeny-independent detection of functional residues

F. Pazos, A. Rausell, Alfonso Valencia, 2006 .

Corrigendum to “Automatic Methods for Predicting Functionally Important Residues” [J. Mol. Biol. 326 (2003) 1289–1302]

Alfonso Valencia, Florencio Pazos, Antonio del Sol, 2009 .

The environmental fate of organic pollutants through the global microbial metabolism

Alfonso Valencia, Florencio Pazos, Víctor de Lorenzo, 2007, Molecular Systems Biology.

Biodegradation Prediction Tools

F. Pazos, V. Lorenzo, 2015 .

New books

Alfonso Valencia, Florencio Pazos, K. V. Ujimoto, 2006, Philosophy.

Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families

Alfonso Valencia, Florencio Pazos, Miguel A. Andrade-Navarro, 1997, BCEC.

Structural basis for the broad specificity of a new family of amino-acid racemases.

F. Pazos, M. Waldor, F. Cava, 2014, Acta crystallographica. Section D, Biological crystallography.

The Oligomerization Domain of VP3, the Scaffolding Protein of Infectious Bursal Disease Virus, Plays a Critical Role in Capsid Assembly

Jose A. Ruiz-Diaz, F. Pazos, J. Castón, 2003, Journal of Virology.

The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain.

A. Valencia, F. Pazos, D. Devos, 2003, European journal of biochemistry.

MBROLE 2.0—functional enrichment of chemical compounds

Monica Chagoyen, Florencio Pazos, Javier López-Ibáñez, 2016, Nucleic Acids Res..

Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes

Florencio Pazos, Daniel Tabas-Madrid, Mònica Franch, 2016, Nucleic Acids Res..

EVA: evaluation of protein structure prediction servers

Marc A. Martí-Renom, Burkhard Rost, Alfonso Valencia, 2003, Nucleic Acids Res..

EVA: continuous automatic evaluation of protein structure prediction servers

Marc A. Martí-Renom, Burkhard Rost, András Fiser, 2001, Bioinform..

The proteome: structure, function and evolution

Michael J E Sternberg, Florencio Pazos, Robert M MacCallum, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

WeReview: CRISPR Tools—Live Repository of Computational Tools for Assisting CRISPR/Cas Experiments

Florencio Pazos, Rafael Torres-Perez, Juan A. Garcia-Martin, 2019, Bioengineering.

New EMBO Member's Review Protein co-evolution, co-adaptation and interactions

Alfonso Valencia, Florencio Pazos, A. Valencia, 2008 .

Genetic polymorphisms among C57BL/6 mouse inbred strains

F. Pazos, J. Benítez, A. González-Neira, 2011, Transgenic Research.

Automatic detection of genomic regions with informative epigenetic patterns

F. Pazos, A. García-Moreno, J. C. Oliveros, 2018, BMC Genomics.

Prediction of protein interaction based on similarity of phylogenetic trees.

Florencio Pazos, David Juan, Jose M G Izarzugaza, 2008, Methods in molecular biology.

Studying the co-evolution of protein families with the Mirrortree web server

Florencio Pazos, David Ochoa, F. Pazos, 2010, Bioinform..

MetaRouter: bioinformatics for bioremediation

Alfonso Valencia, Víctor de Lorenzo, Florencio Pazos, 2004, Nucleic Acids Res..

Bioinformatics Applications Note Systems Biology Mbrole: Enrichment Analysis of Metabolomic Data

Monica Chagoyen, Florencio Pazos, F. Pazos, 2022 .

Network Analysis in Systems Biology

Florencio Pazos, Monica Chagoyen, F. Pazos, 2021 .

Applications of molecular networks in biomedicine

Florencio Pazos, Monica Chagoyen, Juan A. G. Ranea, 2019, Biology methods & protocols.

Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods.

Michael J E Sternberg, Florencio Pazos, Jung-Wook Bang, 2008, Journal of proteome research.

Reactome Array: Forging a Link Between Metabolome and Genome

F. Pazos, K. Timmis, Marta Godoy, 2009, Science.

A platform for integrating threading results with protein family analyses

Burkhard Rost, Alfonso Valencia, Florencio Pazos, 1999, Bioinform..

Tools for the functional interpretation of metabolomic experiments

Monica Chagoyen, Florencio Pazos, F. Pazos, 2013, Briefings Bioinform..

Factors affecting interactome-based prediction of human genes associated with clinical signs

Monica Chagoyen, Florencio Pazos, Sara González-Pérez, 2017, BMC Bioinformatics.

Practical aspects of protein co-evolution

Florencio Pazos, David Ochoa, F. Pazos, 2014, Front. Cell Dev. Biol..

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

Alfonso Valencia, Florencio Pazos, Thilo Muth, 2012, Bioinform..

Computational prediction of protein functional sites-Applications in biotechnology and biomedicine.

F. Pazos, 2022, Advances in protein chemistry and structural biology.

Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity

F. Pazos, 2021, Bioengineering.

Protein residues determining interaction specificity in paralogous families

Florencio Pazos, Juan Garcia Ranea, Borja Pitarch, 2020, Bioinform..

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues

F. Pazos, D. Garrido-Martín, 2018, BMC Bioinformatics.

Practical analysis of specificity-determining residues in protein families

Florencio Pazos, Monica Chagoyen, Juan A. García-Martín, 2016, Briefings Bioinform..

Predicting Protein Interactions

D. Juan, F. Pazos, 2015 .

Selection of organisms for the co-evolution-based study of protein interactions

Alfonso Valencia, Florencio Pazos, Daniel Lopez, 2011, BMC Bioinformatics.

Phylogeny-independent detection of functional residues

Alfonso Valencia, Florencio Pazos, Antonio Rausell, 2006, Bioinform..

Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds

Florencio Pazos, Juan C. Triviño, F. Pazos, 2010, BMC Systems Biology.

DIDO3 acts at the interface of RNAPII transcription and chromatin structure regulation

A. Valencia, T. Pons, F. Pazos, 2021, bioRxiv.

CAFASP3 in the spotlight of EVA

Alfonso Valencia, Florencio Pazos, Burkhard Rost, 2003, Proteins.

TreeDet: a web server to explore sequence space

Alfonso Valencia, Florencio Pazos, Michael L. Tress, 2006, Nucleic Acids Res..

Threading structural model of the manganese‐stabilizing protein PsbO reveals presence of two possible β‐sandwich domains

A. Valencia, F. Pazos, F. Pazos, 2001, Proteins.

Characterization of clinical signs in the human interactome

Monica Chagoyen, Florencio Pazos, F. Pazos, 2016, Bioinform..

CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature.

F. Pazos, M. Chagoyen, Pedro Seoane, 2022, Journal of molecular biology.

Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex

F. Pazos, M. Chagoyen, J. Carrascosa, 2014, Proteins.

EVAcon: a protein contact prediction evaluation service

Burkhard Rost, Alfonso Valencia, Florencio Pazos, 2005, Nucleic Acids Res..

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology

Monica Chagoyen, Florencio Pazos, F. Pazos, 2019, Briefings Bioinform..

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories

Alfonso Valencia, Florencio Pazos, Osvaldo Graña, 2005, Trans. Comp. Sys. Biology.

Detection of significant protein coevolution

Alfonso Valencia, Florencio Pazos, David Ochoa, 2015, Bioinform..

Protein functional features are reflected in the patterns of mRNA translation speed

F. Pazos, Daniel Lopez, 2015, BMC Genomics.

Modelling Inhibition in Metabolic Pathways Through Abduction and Induction

Stephen Muggleton, Antonis C. Kakas, Alireza Tamaddoni-Nezhad, 2004, ILP.

Genome-Wide Analysis of Protein Disorder in Arabidopsis thaliana: Implications for Plant Environmental Adaptation

Florencio Pazos, Natalia Pietrosemoli, F. Pazos, 2013, PloS one.

Towards the prediction of protein interaction partners using physical docking

Alfonso Valencia, Florencio Pazos, Carles Pons, 2011, Molecular systems biology.

Defining functional distances over Gene Ontology

Alfonso Valencia, Florencio Pazos, Angela del Pozo, 2008, BMC Bioinformatics.

Factors affecting interactome-based prediction of human genes associated with clinical signs

F. Pazos, M. Chagoyen, Sara González-Pérez, 2017, BMC Bioinformatics.

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues

Diego Garrido-Martín, Florencio Pazos, F. Pazos, 2018, BMC Bioinformatics.

Ice Age Terminations

W. Broecker, F. Pazos, K. Timmis, 2009, Science.

MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis

F. Pazos, M. Chagoyen, Javier López-Ibáñez, 2023, Nucleic Acids Res..

A platform for integrating threading results with protein family analyses

B. Rost, F. Pazos, Alfonso Valencia, 1999 .

A graphical interface for correlated mutations and other protein structure prediction methods

Alfonso Valencia, Florencio Pazos, O. Olmea, 1997, Comput. Appl. Biosci..

The organization of the microbial biodegradation network from a systems‐biology perspective

A. Valencia, F. Pazos, V. de Lorenzo, 2003, EMBO reports.

The environmental fate of organic pollutants through the global microbial metabolism

F. Pazos, V. Lorenzo, M. J. Gómez, 2007 .

MBRole: enrichment analysis of metabolomic data.

F. Pazos, M. Chagoyen, 2011, Bioinformatics.

Enhancing the prediction of protein pairings between interacting families using orthology information

A. Valencia, D. Juan, F. Pazos, 2008, BMC Bioinform..

Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data

Monica Chagoyen, Florencio Pazos, F. Pazos, 2010, Bioinform..

PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information

F. Pazos, M. Chagoyen, F. J. Moreno, 2023, Genes.

A platform for integrating threading results with protein family analyses

B. Rost, A. Valencia, F. Pazos, 1999, Bioinform..

EVA: evaluation of protein structure prediction servers

B. Rost, A. Valencia, F. Pazos, 2003, Nucleic Acids Res..

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

A. Valencia, D. Juan, F. Pazos, 2008, Proceedings of the National Academy of Sciences.

Reactome Array: Forging a Link Between Metabolome and Genome

F. Pazos, Marta Godoy, Rafael Silva-Rocha, 2009, Science.

TSEMA: interactive prediction of protein pairings between interacting families

Alfonso Valencia, Florencio Pazos, Juan Garcia Ranea, 2006, Nucleic Acids Res..

CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature

F. Pazos, M. Chagoyen, J. A. Garcia-Ranea, 2024, Database : the journal of biological databases and curation.