Baldo Oliva

Summary

Affiliation: Hospital del Mar
Country: Spain

Publications

  1. ncbi request reprint Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
    Jordi Espadaler
    Grup de Bioinformàtica Estructural GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
    Bioinformatics 21:3360-8. 2005
  2. pmc Topological comparison of methods for predicting transcriptional cooperativity in yeast
    Daniel Aguilar
    Structural Bioinformatics Group GRIB, IMIM Universitat Pompeu Fabra, C Doctor Aiguader, 88, Barcelona 08003, Spain
    BMC Genomics 9:137. 2008
  3. pmc Prediction of enzyme function by combining sequence similarity and protein interactions
    Jordi Espadaler
    Laboratori de Bioinformàtica Estructural GRIB, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra IMIM, 08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 9:249. 2008
  4. pmc ModLink+: improving fold recognition by using protein-protein interactions
    Oriol Fornes
    Structural Bioinformatics Lab GRIB IMIM, Universitat Pompeu Fabra, Parc de Recerca Biomédica de Barcelona PRBB, Barcelona, Catalonia, Spain
    Bioinformatics 25:1506-12. 2009
  5. doi request reprint Functional clustering of metastasis proteins describes plastic adaptation resources of breast-cancer cells to new microenvironments
    Berta Martín
    Centre d Oncologia Molecular, IDIBELL, Hospital Duran i Reynals, CSUB, L Hospitalet Llobregat, Barcelona, Spain
    J Proteome Res 7:3242-53. 2008
  6. pmc Characterization of protein hubs by inferring interacting motifs from protein interactions
    Ramon Aragues
    Structural Bioinformatics Lab GRIB, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine PRBB, Barcelona, Catalonia, Spain
    PLoS Comput Biol 3:1761-71. 2007
  7. pmc Expression of endoplasmic reticulum stress proteins is a candidate marker of brain metastasis in both ErbB-2+ and ErbB-2- primary breast tumors
    Rebeca Sanz-Pamplona
    Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute IDIBELL, Barcelona, Spain
    Am J Pathol 179:564-79. 2011
  8. pmc Biana: a software framework for compiling biological interactions and analyzing networks
    Javier Garcia-Garcia
    Structural Bioinformatics Lab, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain
    BMC Bioinformatics 11:56. 2010
  9. ncbi request reprint Underexpression of transcriptional regulators is common in metastatic breast cancer cells overexpressing Bcl-xL
    Olga Mendez
    Centre d Oncologia Molecular, Institut de Recerca Oncologica, IDIBELL, Hospital Duran i Reynals, Gran Via s n, Km 2, 7, E 08907 L Hospitalet Ll, Barcelona, Spain
    Carcinogenesis 27:1169-79. 2006
  10. doi request reprint iLoops: a protein-protein interaction prediction server based on structural features
    Joan Planas-Iglesias
    Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain
    Bioinformatics 29:2360-2. 2013

Collaborators

Detail Information

Publications31

  1. ncbi request reprint Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
    Jordi Espadaler
    Grup de Bioinformàtica Estructural GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
    Bioinformatics 21:3360-8. 2005
    ....
  2. pmc Topological comparison of methods for predicting transcriptional cooperativity in yeast
    Daniel Aguilar
    Structural Bioinformatics Group GRIB, IMIM Universitat Pompeu Fabra, C Doctor Aiguader, 88, Barcelona 08003, Spain
    BMC Genomics 9:137. 2008
    ....
  3. pmc Prediction of enzyme function by combining sequence similarity and protein interactions
    Jordi Espadaler
    Laboratori de Bioinformàtica Estructural GRIB, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra IMIM, 08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 9:249. 2008
    ..Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners...
  4. pmc ModLink+: improving fold recognition by using protein-protein interactions
    Oriol Fornes
    Structural Bioinformatics Lab GRIB IMIM, Universitat Pompeu Fabra, Parc de Recerca Biomédica de Barcelona PRBB, Barcelona, Catalonia, Spain
    Bioinformatics 25:1506-12. 2009
    ..Here, we present an improved version of the method that addresses this limitation. We also compare our method to other state-of-the-art fold assignment methodologies...
  5. doi request reprint Functional clustering of metastasis proteins describes plastic adaptation resources of breast-cancer cells to new microenvironments
    Berta Martín
    Centre d Oncologia Molecular, IDIBELL, Hospital Duran i Reynals, CSUB, L Hospitalet Llobregat, Barcelona, Spain
    J Proteome Res 7:3242-53. 2008
    ..71 x 10(-2)) and protein amino acid phosphorylation (p-value FDR = 3.28 x 10(-2)) might be the most significant biological process differentially increased in liver metastasis...
  6. pmc Characterization of protein hubs by inferring interacting motifs from protein interactions
    Ramon Aragues
    Structural Bioinformatics Lab GRIB, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine PRBB, Barcelona, Catalonia, Spain
    PLoS Comput Biol 3:1761-71. 2007
    ..The proposed method will help us discover unknown interacting motifs and provide biological insights about protein hubs and their roles in interaction networks...
  7. pmc Expression of endoplasmic reticulum stress proteins is a candidate marker of brain metastasis in both ErbB-2+ and ErbB-2- primary breast tumors
    Rebeca Sanz-Pamplona
    Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute IDIBELL, Barcelona, Spain
    Am J Pathol 179:564-79. 2011
    ..16) than ErbB-2 (LR = 0.42). We conclude that, in breast carcinomas, certain proteins associated with the endoplasmic reticulum stress phenotype are candidate markers of brain metastasis...
  8. pmc Biana: a software framework for compiling biological interactions and analyzing networks
    Javier Garcia-Garcia
    Structural Bioinformatics Lab, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain
    BMC Bioinformatics 11:56. 2010
    ..In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties...
  9. ncbi request reprint Underexpression of transcriptional regulators is common in metastatic breast cancer cells overexpressing Bcl-xL
    Olga Mendez
    Centre d Oncologia Molecular, Institut de Recerca Oncologica, IDIBELL, Hospital Duran i Reynals, Gran Via s n, Km 2, 7, E 08907 L Hospitalet Ll, Barcelona, Spain
    Carcinogenesis 27:1169-79. 2006
    ....
  10. doi request reprint iLoops: a protein-protein interaction prediction server based on structural features
    Joan Planas-Iglesias
    Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain
    Bioinformatics 29:2360-2. 2013
    ..The server evaluates the putative interaction using a random forest classifier...
  11. doi request reprint Understanding protein-protein interactions using local structural features
    Joan Planas-Iglesias
    Structural Bioinformatics Group GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, C Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
    J Mol Biol 425:1210-24. 2013
    ..We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable circumstances...
  12. ncbi request reprint Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasis
    Rebeca Sanz
    Centre d Oncologia Molecular, Institut de Recerca Oncològica IDIBELL, Hospital Duran i Reynals, Gran Via, S N, Km 2 7, L Hospitalet Ll, 08907, Barcelona, Spain
    Clin Exp Metastasis 24:673-83. 2007
    ....
  13. pmc ArchDB 2014: structural classification of loops in proteins
    Jaume Bonet
    Structural Bioinformatics Lab GRIB IMIM, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine PRBB, Barcelona, Catalonia, 08950, Spain and Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA Aberystwyth, Ceredigion, UK
    Nucleic Acids Res 42:D315-9. 2014
    ..The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses...
  14. ncbi request reprint Identification of function-associated loop motifs and application to protein function prediction
    Jordi Espadaler
    Group de Bioinformàtica Estructural GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra 08003 Barcelona, Catalonia, Spain
    Bioinformatics 22:2237-43. 2006
    ..This identification can be used on sequence annotations...
  15. pmc Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization
    Emre Guney
    Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain
    PLoS ONE 7:e43557. 2012
    ..Our findings suggest that GUILD helps to identify genes implicated in the pathology of human disorders independent of the loci associated with the disorders...
  16. doi request reprint Extending signaling pathways with protein-interaction networks. Application to apoptosis
    Joan Planas-Iglesias
    Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    OMICS 16:245-56. 2012
    ..We provide our predictions at http://sbi.imim.es/web/Apoptosis.php...
  17. pmc BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference
    Javier Garcia-Garcia
    Structural Bioinformatics Laboratory GRIB IMIM, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine PRBB, 08003 Barcelona, Catalonia, Spain
    Nucleic Acids Res 40:W147-51. 2012
    ..The specificity is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate similarities between sequences. BIPS is freely accessible at http://sbi.imim.es/BIPS.php...
  18. pmc Predicting cancer involvement of genes from heterogeneous data
    Ramon Aragues
    Structural Bioinformatics Lab, GRIB, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine PRBB, 08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 9:172. 2008
    ..Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data...
  19. doi request reprint Analysis of electrostatic contributions to the selectivity of interactions between RING-finger domains and ubiquitin-conjugating enzymes
    Johanna Scheper
    Department of Molecular and Cell Biology, Instituto de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, Barcelona, Spain
    Proteins 74:92-103. 2009
    ..The application of some of these rules of interaction selectivity has permitted us to experimentally manipulate the selectivity of interaction of the RING-finger domain-E2 pairs under study...
  20. pmc Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations
    Patrick Aloy
    Institut de Recerca Biomèdica and Barcelona Supercomputing Center, 10 12 08028 Barcelona, Catalonia, Spain
    BMC Struct Biol 9:71. 2009
    ..The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both...
  21. doi request reprint On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein-Protein, Protein-DNA, and Protein-RNA Interactions
    Oriol Fornes
    Structural Bioinformatics Lab GRIB, Departament de Ciѐncies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
    Adv Protein Chem Struct Biol 94:77-120. 2014
    ..Moreover, we provide ready-to-use resources for docking and benchmarking protein interactions. ..
  22. doi request reprint Protein kinase CK2-dependent phosphorylation of the human Regulators of Calcineurin reveals a novel mechanism regulating the calcineurin-NFATc signaling pathway
    Sergio Martínez-Høyer
    Bellvitge Biomedical Research Institute IDIBELL, L Hospitalet de Llobregat, Barcelona, Catalonia, Spain
    Biochim Biophys Acta 1833:2311-21. 2013
    ..The knowledge of how RCAN proteins modulate the calcineurin-NFATc pathway paves the way for the development of potent novel selective immunosuppressant drugs. ..
  23. ncbi request reprint PIANA: protein interactions and network analysis
    Ramon Aragues
    Structural Bioinformatics Group GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, C Doctor Aiguader, 83, Barcelona 08003, Catalonia, Spain
    Bioinformatics 22:1015-7. 2006
    ..Availability: PIANA is under the GNU GPL. Source code, database and detailed documentation may be freely downloaded from http://sbi.imim.es/piana...
  24. ncbi request reprint GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms
    Emre Guney
    Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group GRIB IMIM, Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain
    Bioinformatics 30:1789-90. 2014
    ..It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies. Availability and implementation: Available online at http://sbi.imim.es/GUILDify.php..
  25. pmc The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site
    Laia Vives-Adrián
    Institut de Biologia Molecular de Barcelona CSIC, Parc Cientific de Barcelona, Barcelona, Spain
    J Virol 88:5595-607. 2014
    ....
  26. pmc Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasis
    Laura España
    Centre d Oncologia Molecular, Institut de Recerca Oncològica IDIBELL, Hosp Duran i Reynals, C S U B, 08907 L Hospitalet de Llobregat, Barcelona, Spain
    Am J Pathol 167:1125-37. 2005
    ..In conclusion, Bcl-x(L) mediates a phenotype in which redox pathways and glycolysis are coupled to protect breast cancer metastatic cells during transit from the primary tumor to the metastatic state...
  27. pmc Functional and topological characterization of transcriptional cooperativity in yeast
    Daniel Aguilar
    Structural Bioinformatics Group, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, C Dr, Aiguader 88, 08003 Barcelona, Spain
    BMC Res Notes 5:227. 2012
    ....
  28. pmc Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features
    Daniel Aguilar
    Structural Bioinformatics Group, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
    PLoS ONE 7:e41430. 2012
    ..Finally, we discovered a significant enrichment of functional residues (e.g. metal binding, susceptibility to detrimental mutations) in the clusters, which could be the foundation of new prediction tools...
  29. ncbi request reprint Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking
    Simon J Cockell
    Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
    Bioinformatics 23:573-81. 2007
    ..Here we describe a novel method that uses structural models to reduce a large number of in silico predictions to a high confidence subset that is amenable to experimental validation...
  30. pmc Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
    Daniel Aguilar
    HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1305 York Ave, New York, NY 10021, USA
    Nucleic Acids Res 36:3728-37. 2008
    ..Since the approach does not use sequence similarity, we expect that TEPSS will be useful for various gene discovery applications. TEPSS programs and data are distributed at http://icb.med.cornell.edu/crt/tepss/index.xml...
  31. doi request reprint Knowledge environments representing molecular entities for the virtual physiological human
    Martin Hofmann-Apitius
    Bonn Aachen International Center for Information Technology, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany
    Philos Trans A Math Phys Eng Sci 366:3091-110. 2008
    ..Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH...